mays_est	Aligning Zea Mays (Maize) ESTs onto the Rice Genome	/*<br>_n_n_This documents the processing of zea mays ESTs to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Mon Mar 25 11:48:03 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The ESTs are from the GenBank nucleotide query &quot;txid4577[orgn]  AND<br>_n_n_gbdiv_est[PROP]&quot;  The average ESTs length is 462.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_1,847 sequences were compared to  147,657 ESTs using BLAT with<br>_n_n_mindIdentity=50.   The 194,774 BLAT hits were filtered using pslReps<br>_n_n_utility with -minAli=0.85 -nearTop=0.01.  This resulted in 113,774<br>_n_n_alignments.<br>_n_n_<br>_n_n_The lengths of the matches are distributed as follows:<br>_n_n_<br>_n_n_Length of<br>_n_n_hits_t_t_     Count<br>_n_n_--------     ------<br>_n_n_0-100_t_t__t_t_22936<br>_n_n_100-150_t_t__t_t_16744<br>_n_n_150-200_t_t__t_t_15256<br>_n_n_200-250_t_t__t_t_13538<br>_n_n_250-300_t_t__t_t_14785<br>_n_n_300-350_t_t__t_t_11878<br>_n_n_350-400_t_t__t_t_9652<br>_n_n_400-450_t_t__t_t_4258<br>_n_n_450-500_t_t__t_t_2373<br>_n_n_500-550_t_t__t_t_1501<br>_n_n_550-600_t_t__t_t_579<br>_n_n_600-650_t_t__t_t_182<br>_n_n_650-700_t_t__t_t_56<br>_n_n_700-750_t_t__t_t_11<br>_n_n_750-800_t_t__t_t_12<br>_n_n_&gt;800_t_t__t_t_13<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Removing matches with less than 150bp match-length leaves 73,771 hits.<br>_n_n_<br>_n_n_Many of the ESTs hit more than once.  The distribution of the hit<br>_n_n_frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_23982<br>_n_n_02_t_t__t_t_11165<br>_n_n_03_t_t__t_t_3571<br>_n_n_04_t_t__t_t_1135<br>_n_n_05_t_t__t_t_459<br>_n_n_06_t_t__t_t_418<br>_n_n_07_t_t__t_t_274<br>_n_n_08_t_t__t_t_139<br>_n_n_09_t_t__t_t_90<br>_n_n_10_t_t__t_t_58<br>_n_n_20_t_t__t_t_204<br>_n_n_40_t_t__t_t_15<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_ESTs that hit more than three times are removed, with 57,025 hits<br>_n_n_remaining.  These matches have the following distribution of the percent<br>_n_n_identity per hit:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_82_t_t__t_t_445<br>_n_n_83_t_t__t_t_1602<br>_n_n_84_t_t__t_t_2512<br>_n_n_85_t_t__t_t_3606<br>_n_n_86_t_t__t_t_4654<br>_n_n_87_t_t__t_t_5710<br>_n_n_88_t_t__t_t_6861<br>_n_n_89_t_t__t_t_7459<br>_n_n_90_t_t__t_t_7263<br>_n_n_91_t_t__t_t_5769<br>_n_n_92_t_t__t_t_4022<br>_n_n_93_t_t__t_t_2744<br>_n_n_94_t_t__t_t_1975<br>_n_n_95_t_t__t_t_1193<br>_n_n_96_t_t__t_t_508<br>_n_n_97_t_t__t_t_245<br>_n_n_98_t_t__t_t_345<br>_n_n_99_t_t__t_t_100<br>_n_n_100_t_t__t_t_12<br>_n_n_<br>_n_n_<br>_n_n_The distribution of the sequenced clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_      Count<br>_n_n_------_t_t_      ----------<br>_n_n_01000_t_t__t_t_48983<br>_n_n_02000_t_t__t_t_5755<br>_n_n_03000_t_t__t_t_1064<br>_n_n_04000_t_t__t_t_250<br>_n_n_05000_t_t__t_t_168<br>_n_n_06000_t_t__t_t_108<br>_n_n_07000_t_t__t_t_45<br>_n_n_08000_t_t__t_t_76<br>_n_n_09000_t_t__t_t_43<br>_n_n_10000_t_t__t_t_43<br>_n_n_20000_t_t__t_t_201<br>_n_n_30000_t_t__t_t_111<br>_n_n_40000_t_t__t_t_116<br>_n_n_50000_t_t__t_t_20<br>_n_n_60000_t_t__t_t_24<br>_n_n_70000_t_t__t_t_15<br>_n_n_&gt;90000_t_t__t_t_3<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 38,718 unique ESTs and 1,625 sequenced clones.<br>_n_n_Those having at least one gap of length 50 or above, are considered<br>_n_n_multi-exon hits.  30,186 are multi-exon and 10,181 are single-exon hits.<br>_n_n_<br>_n_n_	0
hordium_est	Aligning Hordeum Vulgare (Barley) ESTs onto the Rice Genome	/*<br>_n_n_This documents the processing of hordeum vulgare ESTs to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Mon Mar 25 10:15:45 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The ESTs are from the GenBank nucleotide query &quot;txid4558[orgn]  AND<br>_n_n_gbdiv_est[PROP]&quot;  The average ESTs length is 586.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_1,847 sequences were compared to  148,651 ESTs using BLAT with<br>_n_n_mindIdentity=50.   The 302,684 BLAT hits were filtered using pslReps<br>_n_n_utility with -minAli=0.85 -nearTop=0.01.  This resulted in 156,816<br>_n_n_alignments.<br>_n_n_<br>_n_n_The lengths of the matches are distributed as follows:<br>_n_n_<br>_n_n_Length of<br>_n_n_hits_t_t_     Count<br>_n_n_--------     ------<br>_n_n_0-100_t_t__t_t_26422<br>_n_n_100-150_t_t__t_t_14299<br>_n_n_150-200_t_t__t_t_15200<br>_n_n_200-250_t_t__t_t_14398<br>_n_n_250-300_t_t__t_t_14936<br>_n_n_300-350_t_t__t_t_14400<br>_n_n_350-400_t_t__t_t_12691<br>_n_n_400-450_t_t__t_t_10209<br>_n_n_450-500_t_t__t_t_8313<br>_n_n_500-550_t_t__t_t_7644<br>_n_n_550-600_t_t__t_t_7357<br>_n_n_600-650_t_t__t_t_4951<br>_n_n_650-700_t_t__t_t_3022<br>_n_n_700-750_t_t__t_t_1605<br>_n_n_750-800_t_t__t_t_973<br>_n_n_&gt;800_t_t__t_t_396<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Removing matches with less than 150bp match-length leaves 115,830 hits.<br>_n_n_<br>_n_n_Many of the ESTs hit more than once.  The distribution of the hit<br>_n_n_frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_30843<br>_n_n_02_t_t__t_t_14684<br>_n_n_03_t_t__t_t_5052<br>_n_n_04_t_t__t_t_1425<br>_n_n_05_t_t__t_t_726<br>_n_n_06_t_t__t_t_1922<br>_n_n_07_t_t__t_t_2171<br>_n_n_08_t_t__t_t_127<br>_n_n_09_t_t__t_t_65<br>_n_n_10_t_t__t_t_48<br>_n_n_20_t_t__t_t_130<br>_n_n_30_t_t__t_t_15<br>_n_n_40_t_t__t_t_6<br>_n_n_50_t_t__t_t_1<br>_n_n_60_t_t__t_t_2<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_ESTs that hit more than three times are removed, with 75,367 hits<br>_n_n_remaining.  These matches have the following distribution of the percent<br>_n_n_identity per hit:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_82_t_t__t_t_605<br>_n_n_83_t_t__t_t_2212<br>_n_n_84_t_t__t_t_3711<br>_n_n_85_t_t__t_t_5016<br>_n_n_86_t_t__t_t_6550<br>_n_n_87_t_t__t_t_7570<br>_n_n_88_t_t__t_t_8746<br>_n_n_89_t_t__t_t_9476<br>_n_n_90_t_t__t_t_9201<br>_n_n_91_t_t__t_t_7465<br>_n_n_92_t_t__t_t_5414<br>_n_n_93_t_t__t_t_3701<br>_n_n_94_t_t__t_t_2452<br>_n_n_95_t_t__t_t_1598<br>_n_n_96_t_t__t_t_918<br>_n_n_97_t_t__t_t_329<br>_n_n_98_t_t__t_t_162<br>_n_n_99_t_t__t_t_165<br>_n_n_100_t_t__t_t_76<br>_n_n_<br>_n_n_<br>_n_n_The distribution of the sequenced clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_      Count<br>_n_n_------_t_t_      ----------<br>_n_n_01000_t_t__t_t_62260<br>_n_n_02000_t_t__t_t_9418<br>_n_n_03000_t_t__t_t_1979<br>_n_n_04000_t_t__t_t_480<br>_n_n_05000_t_t__t_t_246<br>_n_n_06000_t_t__t_t_182<br>_n_n_07000_t_t__t_t_64<br>_n_n_08000_t_t__t_t_59<br>_n_n_09000_t_t__t_t_21<br>_n_n_10000_t_t__t_t_36<br>_n_n_20000_t_t__t_t_302<br>_n_n_30000_t_t__t_t_150<br>_n_n_40000_t_t__t_t_47<br>_n_n_50000_t_t__t_t_47<br>_n_n_60000_t_t__t_t_43<br>_n_n_70000_t_t__t_t_13<br>_n_n_80000_t_t__t_t_7<br>_n_n_90000_t_t__t_t_4<br>_n_n_&gt;90000_t_t__t_t_9<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 50,579 unique ESTs and 1,705 sequenced clones.<br>_n_n_Those having at least one gap of length 50 or above, are considered<br>_n_n_multi-exon hits.  40,400 are multi-exon and 12,482 are single-exon hits.<br>_n_n_<br>_n_n_	0
vocabulary	Controlled Vocabulary Database	_n_n__n_n_<p><b><font face="Arial,Helvetica">Objectives:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1><a target="external" href="/index.html">Gramene</a> _n_n_is a comparative genome database for cereal crops and a community resource_n_n_for rice. We are populating and curating Gramene with annotated sequence_n_n_data and associated biological information including mutants, phenotypes,_n_n_polymorphisms and Quantitative Trait Loci. In order to support queries_n_n_across various data sets as well as across external databases, Gramene_n_n_is employing three related controlled vocabularies. First is the <a target="external" href="/plant_ontology/">Trait_n_n_Ontology</a> (TO) will be implemented across the cereal crops and plants_n_n_to curate and evaluate phenotype comparisons. An initial vocabulary for_n_n_TO and definitions for TO terms is available <a target="external" href="/plant_ontology/">here</a>._n_n_Second is a Plant Ontology (PO) will facilitate the curation of morphological_n_n_and anatomical feature information with respect to expression and localization_n_n_of gene and gene products. The TO and PO are both in the early stages of_n_n_development in collaboration with International Rice Research Institute,_n_n_TAIR, MaizeDB, International Crop Information System and CIMMYT. Finally,_n_n_as part of the <a target="external" href="http://www.geneontology.org">Gene Ontology consortium</a>,_n_n_we will classify confirmed or predicted rice gene products. The development_n_n_of plant specific vocabularies is open for community discussion.</font></font>_n_n_<br>&nbsp;_n_n_<p><b><font face="Arial,Helvetica">Ontology database search:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>The ontology search page&nbsp;_n_n_is divided into two sections. The first section allows you to query the&nbsp;_n_n_various terms&nbsp; and data sets contained in our ontology database. The_n_n_second is in interface that displays and allows navigation of the ontology_n_n_terms and their relations. Presently the data sets available for query_n_n_are Trait Ontology<sup>TM</sup> (TO) for rice and the Gene Ontology<sup>TM</sup>_n_n_terms mirrored from http://www.geneontology.org</font></font>_n_n_<p><b><font face="Arial,Helvetica">Ontology Search Section:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>In order to search for a_n_n_term type in term ID or keyword [e.g. cold tolerance or 303]</font></font>_n_n_<p><img SRC="../images/icons/303Help.jpg" height=55 width=600>_n_n_<p><img SRC="../images/icons/CTol.jpg" height=53 width=600>_n_n_<p><b><font face="Arial,Helvetica">Ontology Display Section:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>This is the major part of_n_n_ontology browser and displays one TO/GO term at a time, along with</font></font>_n_n_<br><font face="Arial,Helvetica"><font size=-1>various additional contextual_n_n_data such as term ID, synonym and definition.</font></font>_n_n_<p><img SRC="../images/icons/TO-screen.jpg" height=321 width=600>_n_n_<p><b><font face="Arial,Helvetica">Term Name:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>This is the primary name_n_n_assigned to this term by either the Gramene curator_n_n_for the rice TO or the GO consortium. It is intended to be</font></font>_n_n_<font face="Arial,Helvetica"><font size=-1>sufficient to describe the_n_n_term without requiring any further reference to the structure of_n_n_the ontology.</font></font>_n_n_<p><b><font face="Arial,Helvetica">Term ID:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>This is the accession number_n_n_of this term. TO accessions are in the form '</font><b>TO:</b><font size=-1>'&nbsp;_n_n_and&nbsp; GO accessions are in the form '</font><b>GO:</b><font size=-1>'_n_n_followed by exactly seven decimal digits e.g. (<a target="external" href="/perl/ontology/search_term?id=TO:0000303">TO:0000303</a>),_n_n_(<a target="external" href="/perl/ontology/search_term?id=GO:0006818">GO:0006818</a>)</font></font>_n_n_<p><b><font face="Arial,Helvetica">Synonyms (optional):</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>The synonyms are other alternate_n_n_	0
vocabulary	Controlled Vocabulary Database	names for this term. If there are no synonyms for the term you're viewing_n_n_then this box won't be present - the same applies to all the potentially_n_n_optional fields in the display.</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>for example</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>%cold tolerance ; TO:0000303_n_n_; synonym:CTol</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>OR</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>%cytoplasmic male sterility_n_n_type ; TO:0000232 ; synonym:MaizeDB-64827 ; synonym:CMS</font></font>_n_n_<p><b><font face="Arial,Helvetica">Definition:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>The optional definition,_n_n_if present, describes the term in more detail. TO / GO definitions are</font></font>_n_n_<br><font face="Arial,Helvetica"><font size=-1>drawn from a variety of_n_n_sources.</font></font>_n_n_<p><font size=-1>for example</font>_n_n_<p><font size=-1>term: 100-grain weight</font>_n_n_<br><font size=-1>goid: TO:0000269</font>_n_n_<br><font size=-1>definition: measurements in grams of 100 well-developed_n_n_whole grains, dried to 13% moisture content, weight on a precision balance._n_n_Determine at growth stage 9</font>_n_n_<br><font size=-1>definition_reference: <a target="external" href="http://www.riceweb.org/ses/sesidx.htm">IRRI:SES</a></font>_n_n_<br><font size=-1>definition_reference: GR:pj37 (curator)</font>_n_n_<p><b><font face="Arial,Helvetica">Lineage: Derivation</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>This box is always present,_n_n_and shows every possible path back from the selected term&nbsp; to the_n_n_root. Due to the 'strong path' property of the TO/GO, the implication is_n_n_that if a given trait term / gene product has been assigned an ID, it is_n_n_also implicitly mapped to all</font></font>_n_n_<font face="Arial,Helvetica"><font size=-1>the terms shown in this_n_n_display. Clicking on any of the terms in the lineage will select that term_n_n_as the current&nbsp; displayed term and refresh the window.</font></font>_n_n_<p><b><font face="Arial,Helvetica">Term Relationships:</font></b>_n_n_<p><b><font face="Arial,Helvetica"><font size=-1>Parent and Child terms:</font></font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>These boxes display the_n_n_immediate parents-children relationship of the currently selected term.</font></font>_n_n_<br>&nbsp;_n_n_<blockquote>_n_n_<blockquote><font face="Arial,Helvetica"><font size=-1>Parent-child relationships_n_n_between terms are represented by indentation:</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>&nbsp; parent_term</font></font>_n_n_<br><font face="Arial,Helvetica"><font size=-1>&nbsp;&nbsp;&nbsp; child_term</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>Instance relationship: (marked_n_n_by "</font><b>%</b><font size=-1>" percentage sign in the flat text files_n_n_or by </font><b>[i]</b><font size=-1> in the Ontology browser section)</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>&nbsp; %term0</font></font>_n_n_<br><font face="Arial,Helvetica"><font size=-1>&nbsp;&nbsp;&nbsp; %term1_n_n_% term2</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>To be read as term1 being_n_n_an instance of term0 and also an instance of term2 and term3. Part of relationship:_n_n_(marked by "</font><b>&lt;</b><font size=-1>" less than sign in the flat text files or by </font><b>[p]</b><font size=-1>_n_n_in the Ontology browser section)</font></font>_n_n_<p><font face="Arial,Helvetica"><font size=-1>&nbsp; %term0</font></font>_n_n_<br><font face="Arial,Helvetica"><font size=-1>&nbsp;&nbsp;&nbsp; %term1_n_n_&lt; term2 &lt; term3</font></font></blockquote>_n_n_</blockquote>_n_n_<font size=-1>&nbsp;&nbsp; An example from a flat file:</font>_n_n_<blockquote><font size=-1>&lt;fertility or sterility trait ; TO:0000392_n_n_&lt; whole plant related trait ; TO:0000398</font>_n_n_<br><font size=-1>&nbsp; %fertility related trait ; TO:0000497</font>_n_n_<br><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp; %female fertility restoration_n_n_trait ; TO:0000498</font>_n_n_	1
mutantsubmission	Mutant online submission form	_n_n_<table BORDER=0 CELLSPACING=0 CELLPADDING=0 WIDTH="100%" >_n_n_<tr>_n_n_<td class="submitsubheader">&nbsp;</td>_n_n_</tr>_n_n__n_n_<tr ALIGN=LEFT>_n_n_<td class="submitsubheader">Please use <a target="external" href="/mutant/submission">this form</a> to suggest new terms for_n_n_the rice mutant.  A confirmation email will be sent to you by our curators_n_n_within three days.</td>_n_n_</tr>_n_n_</table>_n_n__n_n_<table BORDER=0 CELLSPACING=0 CELLPADDING=5 WIDTH="100%" >_n_n_<tr>_n_n_<td COLSPAN="2" class="submitsubheadersmall"><b><i>Note: Fields with asterisks_n_n_(*) are mandatory.</i></b></td>_n_n__n_n_  _n_n_</tr>_n_n_</table>_n_n__n_n_<p><h2>Basic Rice Mutant Information</h2>_n_n_<p><a NAME="mutant_name"></a><b>*Mutant Name:</b> Type the full name_n_n_for the mutant. Also give the gene symbol for the mutant.&nbsp;_n_n_<p><a NAME="description"></a><b>*Phynotypic Description:</b> A text_n_n_describing the phenotype for the mutant._n_n_<p><a NAME="other_description"></a><b>Other Description:</b> A text describing mutagenesis_n_n_technique, genetic background, environmental condition related with the_n_n_mutant._n_n_<br>&nbsp;_n_n_<p><h2>Reference for the Rice Mutant</h2>_n_n_<p><a NAME="ref_category"></a><b> Ref. Category:</b> Mention the_n_n_documentary evidence for the mutant, for example, published or personal_n_n_communication. The option "curator" is for internal use._n_n_<br><a NAME="curator"></a><b> Curator:</b> do not select unless you have_n_n_been authorized as a curator by the Gramene._n_n_<br><a NAME="ref_source"></a><b>Ref. Source:</b> If the option "published"_n_n_is selected in the "Reference category", then select from the drop of menu,_n_n_the source of publication, whether it is_n_n_<ul>_n_n_<li>_n_n_<u>PubMed:</u> if an article is available from PubMed.</li>_n_n__n_n_<li>_n_n_<u>AGRICOLA</u>: if an article is available from AGRICOLA.</li>_n_n__n_n_<li>_n_n_<u>BIOSIS previews</u>: if an article is available from BIOSIS previews.</li>_n_n__n_n_<li>_n_n_<u>CAB abstracts</u>: if an article is available from CAB abstracts.</li>_n_n__n_n_<li>_n_n_<u>ISBN:</u> Mention the ISBN number of the publication, published Journal_n_n_(if not listed by PubMed) or Book.&nbsp;</li>_n_n__n_n_<li>_n_n_<u>Web site:</u> if the information is presented on a web site, preferably_n_n_authored by a scientist or hosted by a scientific institution.</li>_n_n__n_n_<li>_n_n_<u>Database:</u> if the information is available from a scientific database_n_n_e.g. TAIR, SGD, MIPS, GenBank, EMBL, Expasy, etc.</li>_n_n__n_n_<br><u>Others</u>: Carefully select this option if any of the above does_n_n_not apply, as this will help our curators in asserting a quality check_n_n_on your contribution.</ul>_n_n_<a NAME="ref_details"></a><b>Reference details:</b> please provide_n_n_the complete citation for the reference which should be cited for the mutant._n_n_It should include author, year, title, journal title, volume, page, etc._n_n_<br>&nbsp;_n_n_<p><h2>Linkeage Rice Map Information_n_n_(If known)</h2>_n_n_<p><a NAME="map_study"></a><b> Map Study:</b> Please select one map study_n_n_which can be used to describe the map position for the mutant._n_n_<ul><b>Please specify if "Other":</b> Please select this option if any_n_n_of the above map studies do not apply. Try to give following information_n_n_on map study: parents for the mapping population, population type (F2 or_n_n_F3 family, DH, RI, etc.), and details of the reference.</ul>_n_n_<a NAME="chromosome_number"></a><b> Chromosome number: </b>Please select the chromosome_n_n_number which the mutant map position is located<b>.</b>_n_n_<br><a NAME="chromosome_location"></a><b> Location on chromosome: </b>Please give_n_n_cM location on the specific map<b>.</b>_n_n_<br><a NAME="marker"></a><b> Linked marker(s): </b>Type the name of_n_n_the linked markers together with the distance between the specific marker_n_n_and mutant locus, eg. RG9 (5.5 cM)._n_n_<br><b></b>&nbsp;<b></b>_n_n_<p><a NAME="contributor"></a><h2>Contributor Information:</h2>_n_n_Please provide information about yourself, to help us identify your contribution. Your valuable contribution will_n_n_be cited, if found appropriate. The mandatory (*) fields_n_n_are:_n_n_<blockquote>Last (Family) name_n_n_<br>First name_n_n_<br>Organization/institution_n_n_<br>Address_n_n_<br>City_n_n_<br>Country_n_n_<br>Email</blockquote>_n_n_	0
mutantsubmission	Mutant online submission form	_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<p>&nbsp;</td>_n_n_</tr>_n_n_</table>_n_n__n_n__n_n_	1
mapviewer	Map Viewer Correspondences	_n_n_<p>A correspondence is an assertion that two markers from one or more maps are the same._n_n_<h2>Genetic Maps</h2>_n_n_<p>_n_n_The equivalences are established based on marker-name identities or in silico analysis.  The majority of the relationships are derived strictly from marker-name indentities, as is the case for all of the non-rice links._n_n_<p>_n_n__t_t_    The sequence comparisons were performed for Cornell and JRGP genetic markers.  This analysis identified equivalent markers not only between, but also within each of the maps.  Viewing the Cornell and JRGP chromosome 7 maps gives a good <a target="external" href="/maps/viewer?start=49&end=67&highlight=&comparative_map1=map_id%3D7&reference_map_study_id=2&reference_map_id=31&start=50&end=67">example</a>.  The JRGP markers C11393s and E10074s have a line connecting them because they share a 185bp region with 99% identity.  Meanwhile, the RZ886 Cornell marker is 100% identical over a 379bp region to JRGP's S11250 marker._n_n_<p>For more information on the marker-marker relationships, please see the documentation for "<a target="external" href="/documentation/marker_marker_documentation.txt">Establishing marker-marker correspondences</a>"._n_n_</p>_n_n_<h2>FPC Data</h2>_n_n_<p>_n_n_The Fingerprint Contigs (FPC) map for rice has been constructed by the <a target="external" href="http://www.genome.clemson.edu/">CUGI group</a>, and genetic markers have been positioned onto individual BACs by hybridization to high density BAC filters.  Correspondences to the genetic maps are based on marker name identities.  While the FPC data is very valuable, it is important to keep in mind that interpretation of the hybridization signals from the BAC filters and the generation of BAC clones clusters (contigs) is inherently error-prone at this stage of the rice seqeuncing project.   _n_n__n_n_<p>In addition to the marker relationships, the FPC map is a way to navigate from plant genetic maps into the Rice genome.  When viewing any one <a target="external" href="/maps/contig?contig_map_id=216;genetic_map_id=31">contig</a> together with a genetic map, small vertical lines appear alongside the contig.  These represent sequenced rice clones that have been placed on the FPC map by CUGI using simulated digest.  These lines link directly into the corresponding clones in the Genome Viewer._n_n__n_n_<p>For more information on the Rice FPC map please go to <a target="external" href="http://www.genome.clemson.edu/projects/rice/fpc">CUGI Physical Maps (FPC Contigs)</a>._n_n_</p>_n_n__n_n_	0
unigene_mays	Aligning Unigene Zea Mays (Maize) EST Clusters onto the Rice Genome	/*<br>_n_n_This documents the processing of zea mays Clusters and ESTs to the<br>_n_n_rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Mon Mar 25 13:52:19 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The Dupont Unigene set is from<br>_n_n_http://www.agron.missouri.edu/files_dl/MMP/Cornsensus.fasta  The average<br>_n_n_Clusters and ESTs length is 1,000.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_1,847 sequences were compared to  10,678 Clusters and ESTs using BLAT<br>_n_n_with mindIdentity=50.   The 13,242 BLAT hits were filtered using<br>_n_n_pslReps utility with -minAli=0.85 -nearTop=0.01.  This resulted in<br>_n_n_7,638 alignments.<br>_n_n_<br>_n_n_The lengths of the matches are distributed as follows:<br>_n_n_<br>_n_n_Length of<br>_n_n_hits_t_t_     Count<br>_n_n_--------     ------<br>_n_n_0-100_t_t__t_t_1106<br>_n_n_100-150_t_t__t_t_784<br>_n_n_150-200_t_t__t_t_749<br>_n_n_200-250_t_t__t_t_703<br>_n_n_250-300_t_t__t_t_641<br>_n_n_300-350_t_t__t_t_566<br>_n_n_350-400_t_t__t_t_516<br>_n_n_400-450_t_t__t_t_386<br>_n_n_450-500_t_t__t_t_312<br>_n_n_500-550_t_t__t_t_268<br>_n_n_550-600_t_t__t_t_203<br>_n_n_600-650_t_t__t_t_200<br>_n_n_650-700_t_t__t_t_176<br>_n_n_700-750_t_t__t_t_142<br>_n_n_750-800_t_t__t_t_119<br>_n_n_&gt;800_t_t__t_t_767<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Removing matches with less than 150bp match-length leaves 5,734 hits.<br>_n_n_<br>_n_n_Many of the Clusters and ESTs hit more than once.  The distribution of<br>_n_n_the hit frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_2704<br>_n_n_02_t_t__t_t_1050<br>_n_n_03_t_t__t_t_218<br>_n_n_04_t_t__t_t_44<br>_n_n_05_t_t__t_t_12<br>_n_n_06_t_t__t_t_4<br>_n_n_07_t_t__t_t_1<br>_n_n_09_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Clusters and ESTs that hit more than three times are removed, with 5,458<br>_n_n_hits remaining.  These matches have the following distribution of the<br>_n_n_percent identity per hit:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_82_t_t__t_t_57<br>_n_n_83_t_t__t_t_225<br>_n_n_84_t_t__t_t_382<br>_n_n_85_t_t__t_t_504<br>_n_n_86_t_t__t_t_607<br>_n_n_87_t_t__t_t_704<br>_n_n_88_t_t__t_t_703<br>_n_n_89_t_t__t_t_714<br>_n_n_90_t_t__t_t_605<br>_n_n_91_t_t__t_t_407<br>_n_n_92_t_t__t_t_263<br>_n_n_93_t_t__t_t_143<br>_n_n_94_t_t__t_t_71<br>_n_n_95_t_t__t_t_41<br>_n_n_96_t_t__t_t_18<br>_n_n_97_t_t__t_t_7<br>_n_n_98_t_t__t_t_6<br>_n_n_99_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_The distribution of the sequenced clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_      Count<br>_n_n_------_t_t_      ----------<br>_n_n_01000_t_t__t_t_3403<br>_n_n_02000_t_t__t_t_1153<br>_n_n_03000_t_t__t_t_512<br>_n_n_04000_t_t__t_t_179<br>_n_n_05000_t_t__t_t_80<br>_n_n_06000_t_t__t_t_25<br>_n_n_07000_t_t__t_t_35<br>_n_n_08000_t_t__t_t_10<br>_n_n_09000_t_t__t_t_9<br>_n_n_10000_t_t__t_t_6<br>_n_n_20000_t_t__t_t_25<br>_n_n_30000_t_t__t_t_6<br>_n_n_40000_t_t__t_t_5<br>_n_n_50000_t_t__t_t_4<br>_n_n_60000_t_t__t_t_2<br>_n_n_70000_t_t__t_t_1<br>_n_n_80000_t_t__t_t_1<br>_n_n_&gt;90000_t_t__t_t_2<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 3,972 unique Clusters and ESTs and 1,488 sequenced<br>_n_n_clones.  Those having at least one gap of length 50 or above,<br>_n_n_are considered multi-exon hits.  3,599 are multi-exon and 471 are<br>_n_n_single-exon hits.<br>_n_n_<br>_n_n_	0
triticum_est	Aligning Triticum Aestivum (Wheat) ESTs onto the Rice Genome	/*<br>_n_n_This documents the processing of triticum aestivum ESTs to the rice<br>_n_n_genome.<br>_n_n_Lenny Teytelman<br>_n_n_Mon Mar 25 10:54:39 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The ESTs are from the GenBank nucleotide query &quot;txid4565[orgn]  AND<br>_n_n_gbdiv_est[PROP]&quot;  The average ESTs length is 475.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_1,847 sequences were compared to  73,395 ESTs using BLAT with<br>_n_n_mindIdentity=50.   The 129,990 BLAT hits were filtered using pslReps<br>_n_n_utility with -minAli=0.85 -nearTop=0.01.  This resulted in 72,132<br>_n_n_alignments.<br>_n_n_<br>_n_n_The lengths of the matches are distributed as follows:<br>_n_n_<br>_n_n_Length of<br>_n_n_hits_t_t_     Count<br>_n_n_--------     ------<br>_n_n_0-100_t_t__t_t_15737<br>_n_n_100-150_t_t__t_t_9448<br>_n_n_150-200_t_t__t_t_9050<br>_n_n_200-250_t_t__t_t_7614<br>_n_n_250-300_t_t__t_t_8630<br>_n_n_300-350_t_t__t_t_7024<br>_n_n_350-400_t_t__t_t_6043<br>_n_n_400-450_t_t__t_t_3999<br>_n_n_450-500_t_t__t_t_2314<br>_n_n_500-550_t_t__t_t_1162<br>_n_n_550-600_t_t__t_t_567<br>_n_n_600-650_t_t__t_t_214<br>_n_n_650-700_t_t__t_t_165<br>_n_n_700-750_t_t__t_t_122<br>_n_n_750-800_t_t__t_t_14<br>_n_n_&gt;800_t_t__t_t_29<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Removing matches with less than 150bp match-length leaves 46,799 hits.<br>_n_n_<br>_n_n_Many of the ESTs hit more than once.  The distribution of the hit<br>_n_n_frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_15224<br>_n_n_02_t_t__t_t_6984<br>_n_n_03_t_t__t_t_2393<br>_n_n_04_t_t__t_t_672<br>_n_n_05_t_t__t_t_173<br>_n_n_06_t_t__t_t_190<br>_n_n_07_t_t__t_t_198<br>_n_n_08_t_t__t_t_85<br>_n_n_09_t_t__t_t_54<br>_n_n_10_t_t__t_t_56<br>_n_n_20_t_t__t_t_110<br>_n_n_30_t_t__t_t_31<br>_n_n_40_t_t__t_t_2<br>_n_n_50_t_t__t_t_1<br>_n_n_60_t_t__t_t_7<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_ESTs that hit more than three times are removed, with 36,371 hits<br>_n_n_remaining.  These matches have the following distribution of the percent<br>_n_n_identity per hit:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_82_t_t__t_t_294<br>_n_n_83_t_t__t_t_1004<br>_n_n_84_t_t__t_t_1597<br>_n_n_85_t_t__t_t_2208<br>_n_n_86_t_t__t_t_2859<br>_n_n_87_t_t__t_t_3344<br>_n_n_88_t_t__t_t_3895<br>_n_n_89_t_t__t_t_4341<br>_n_n_90_t_t__t_t_4544<br>_n_n_91_t_t__t_t_3907<br>_n_n_92_t_t__t_t_3308<br>_n_n_93_t_t__t_t_2175<br>_n_n_94_t_t__t_t_1520<br>_n_n_95_t_t__t_t_745<br>_n_n_96_t_t__t_t_331<br>_n_n_97_t_t__t_t_111<br>_n_n_98_t_t__t_t_64<br>_n_n_99_t_t__t_t_77<br>_n_n_100_t_t__t_t_47<br>_n_n_<br>_n_n_<br>_n_n_The distribution of the sequenced clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_      Count<br>_n_n_------_t_t_      ----------<br>_n_n_01000_t_t__t_t_29972<br>_n_n_02000_t_t__t_t_4602<br>_n_n_03000_t_t__t_t_1010<br>_n_n_04000_t_t__t_t_266<br>_n_n_05000_t_t__t_t_109<br>_n_n_06000_t_t__t_t_81<br>_n_n_07000_t_t__t_t_47<br>_n_n_08000_t_t__t_t_22<br>_n_n_09000_t_t__t_t_11<br>_n_n_10000_t_t__t_t_6<br>_n_n_20000_t_t__t_t_101<br>_n_n_30000_t_t__t_t_50<br>_n_n_40000_t_t__t_t_31<br>_n_n_50000_t_t__t_t_30<br>_n_n_60000_t_t__t_t_10<br>_n_n_70000_t_t__t_t_15<br>_n_n_80000_t_t__t_t_1<br>_n_n_90000_t_t__t_t_2<br>_n_n_&gt;90000_t_t__t_t_5<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 24,601 unique ESTs and 1,635 sequenced clones.<br>_n_n_Those having at least one gap of length 50 or above, are considered<br>_n_n_multi-exon hits.  19,406 are multi-exon and 6,163 are single-exon hits.<br>_n_n_<br>_n_n_	0
bacend	Mapping the CUGI Bacends onto the Rice Genome	/*<br>_n_n_This documents the processing of oryza sativa BACends to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Sun Mar 24 21:03:14 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from GenBenk Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The CUGI BACends are  from the GenBank nucleotide query &quot;(CUGI Rice BAC<br>_n_n_end) AND (oryza [ORGN])&quot;  The average BACends length is 620.<br>_n_n_<br>_n_n_The BACends were masked using RepeatMasker for arabidopsis and grasses<br>_n_n_repeat libraries.<br>_n_n_<br>_n_n_1,847 sequences were compared to  88,053 BACends using BLAT with<br>_n_n_minScore=160.   The results containted a total of 2,065,620 hits.<br>_n_n_<br>_n_n_Real matches should not have huge gaps.  The distribution of the sequenced<br>_n_n_clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length        Count<br>_n_n_------        ----------<br>_n_n_&lt;010_t_t__t_t_1027211<br>_n_n_&lt;020_t_t__t_t_234484<br>_n_n_&lt;030_t_t__t_t_133041<br>_n_n_&lt;040_t_t__t_t_89206<br>_n_n_&lt;050_t_t__t_t_62271<br>_n_n_&lt;060_t_t__t_t_49414<br>_n_n_&lt;070_t_t__t_t_42328<br>_n_n_&lt;080_t_t__t_t_35388<br>_n_n_&lt;090_t_t__t_t_29602<br>_n_n_&lt;100_t_t__t_t_23989<br>_n_n_&lt;200_t_t__t_t_126542<br>_n_n_&lt;300_t_t__t_t_51897<br>_n_n_&lt;400_t_t__t_t_31779<br>_n_n_&lt;500_t_t__t_t_17379<br>_n_n_&lt;600_t_t__t_t_6109<br>_n_n_&lt;700_t_t__t_t_4286<br>_n_n_&lt;800_t_t__t_t_3755<br>_n_n_&lt;900_t_t__t_t_2731<br>_n_n_&gt;900_t_t__t_t_94208<br>_n_n_<br>_n_n_<br>_n_n_Selecting only matches with gap length up to 20 base pairs leaves<br>_n_n_1,277,263 entries.  The true hits should also extend over the whole<br>_n_n_BACends, unless the hit is at the very end or beginning of a BAC/PAC.<br>_n_n_The following is the distribution of the percentage coverage for the<br>_n_n_BACends:<br>_n_n_<br>_n_n_% of BACends<br>_n_n_matched    Count<br>_n_n_--------   ------<br>_n_n_10-19_t_t__t_t_899<br>_n_n_20-29_t_t__t_t_81238<br>_n_n_30-39_t_t__t_t_135453<br>_n_n_40-49_t_t__t_t_134496<br>_n_n_50-59_t_t__t_t_117458<br>_n_n_60-69_t_t__t_t_116940<br>_n_n_70-79_t_t__t_t_137645<br>_n_n_80-84_t_t__t_t_117684<br>_n_n_85-89_t_t__t_t_143694<br>_n_n_90_t_t__t_t_35733<br>_n_n_91_t_t__t_t_36600<br>_n_n_92_t_t__t_t_38391<br>_n_n_93_t_t__t_t_38663<br>_n_n_94_t_t__t_t_35556<br>_n_n_95_t_t__t_t_29782<br>_n_n_96_t_t__t_t_22894<br>_n_n_97_t_t__t_t_18363<br>_n_n_98_t_t__t_t_16277<br>_n_n_99_t_t__t_t_15883<br>_n_n_=100_t_t__t_t_3614<br>_n_n_<br>_n_n_<br>_n_n_Discarding entries that have BACends match coverage less than 96% and<br>_n_n_start/stop more than 20bp away from the BAC/PAC edge, 138,880 entries<br>_n_n_are left.  In these, the percent identity of the matching blocks is<br>_n_n_distributed as follows:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_88_t_t__t_t_169<br>_n_n_89_t_t__t_t_1667<br>_n_n_90_t_t__t_t_3761<br>_n_n_91_t_t__t_t_5643<br>_n_n_92_t_t__t_t_6985<br>_n_n_93_t_t__t_t_7944<br>_n_n_94_t_t__t_t_9020<br>_n_n_95_t_t__t_t_17224<br>_n_n_96_t_t__t_t_19312<br>_n_n_97_t_t__t_t_18551<br>_n_n_98_t_t__t_t_19234<br>_n_n_99_t_t__t_t_20152<br>_n_n_100_t_t__t_t_9218<br>_n_n_<br>_n_n_<br>_n_n_Filtering out the matches with less than 97% identity leaves 67,155.<br>_n_n_<br>_n_n_Many of the BACends hit more than once.  The distribution of the hit<br>_n_n_frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_11686<br>_n_n_02_t_t__t_t_3287<br>_n_n_03_t_t__t_t_1129<br>_n_n_04_t_t__t_t_530<br>_n_n_05_t_t__t_t_243<br>_n_n_06_t_t__t_t_192<br>_n_n_07_t_t__t_t_210<br>_n_n_08_t_t__t_t_317<br>_n_n_09_t_t__t_t_161<br>_n_n_10_t_t__t_t_159<br>_n_n_20_t_t__t_t_493<br>_n_n_30_t_t__t_t_261<br>_n_n_40_t_t__t_t_147<br>_n_n_50_t_t__t_t_49<br>_n_n_60_t_t__t_t_29<br>_n_n_70_t_t__t_t_50<br>_n_n_80_t_t__t_t_31<br>_n_n_90_t_t__t_t_28<br>_n_n_&gt;90_t_t__t_t_44<br>_n_n_<br>_n_n_<br>_n_n_BACends that hit more than three times are removed, with 18,260 hits<br>_n_n_remaining.  These went into the Gramene Sequence Viewer.<br>_n_n_<br>_n_n_	0
BAC_mapping	Mapping the CUGI Bacends onto the Rice Genome	/*<br>_n_n_This documents the processing of oryza sativa BACends to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Sun Mar 24 21:03:14 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from GenBenk Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The CUGI BACends are  from the GenBank nucleotide query &quot;(CUGI Rice BAC<br>_n_n_end) AND (oryza [ORGN])&quot;  The average BACends length is 620.<br>_n_n_<br>_n_n_The BACends were masked using RepeatMasker for arabidopsis and grasses<br>_n_n_repeat libraries.<br>_n_n_<br>_n_n_1,847 sequences were compared to  88,053 BACends using BLAT with<br>_n_n_minScore=160.   The results containted a total of 2,065,620 hits.<br>_n_n_<br>_n_n_Real matches should not have huge gaps.  The distribution of the sequenced<br>_n_n_clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length        Count<br>_n_n_------        ----------<br>_n_n_&lt;010_t_t__t_t_1027211<br>_n_n_&lt;020_t_t__t_t_234484<br>_n_n_&lt;030_t_t__t_t_133041<br>_n_n_&lt;040_t_t__t_t_89206<br>_n_n_&lt;050_t_t__t_t_62271<br>_n_n_&lt;060_t_t__t_t_49414<br>_n_n_&lt;070_t_t__t_t_42328<br>_n_n_&lt;080_t_t__t_t_35388<br>_n_n_&lt;090_t_t__t_t_29602<br>_n_n_&lt;100_t_t__t_t_23989<br>_n_n_&lt;200_t_t__t_t_126542<br>_n_n_&lt;300_t_t__t_t_51897<br>_n_n_&lt;400_t_t__t_t_31779<br>_n_n_&lt;500_t_t__t_t_17379<br>_n_n_&lt;600_t_t__t_t_6109<br>_n_n_&lt;700_t_t__t_t_4286<br>_n_n_&lt;800_t_t__t_t_3755<br>_n_n_&lt;900_t_t__t_t_2731<br>_n_n_&gt;900_t_t__t_t_94208<br>_n_n_<br>_n_n_<br>_n_n_Selecting only matches with gap length up to 20 base pairs leaves<br>_n_n_1,277,263 entries.  The true hits should also extend over the whole<br>_n_n_BACends, unless the hit is at the very end or beginning of a BAC/PAC.<br>_n_n_The following is the distribution of the percentage coverage for the<br>_n_n_BACends:<br>_n_n_<br>_n_n_% of BACends<br>_n_n_matched    Count<br>_n_n_--------   ------<br>_n_n_10-19_t_t__t_t_899<br>_n_n_20-29_t_t__t_t_81238<br>_n_n_30-39_t_t__t_t_135453<br>_n_n_40-49_t_t__t_t_134496<br>_n_n_50-59_t_t__t_t_117458<br>_n_n_60-69_t_t__t_t_116940<br>_n_n_70-79_t_t__t_t_137645<br>_n_n_80-84_t_t__t_t_117684<br>_n_n_85-89_t_t__t_t_143694<br>_n_n_90_t_t__t_t_35733<br>_n_n_91_t_t__t_t_36600<br>_n_n_92_t_t__t_t_38391<br>_n_n_93_t_t__t_t_38663<br>_n_n_94_t_t__t_t_35556<br>_n_n_95_t_t__t_t_29782<br>_n_n_96_t_t__t_t_22894<br>_n_n_97_t_t__t_t_18363<br>_n_n_98_t_t__t_t_16277<br>_n_n_99_t_t__t_t_15883<br>_n_n_=100_t_t__t_t_3614<br>_n_n_<br>_n_n_<br>_n_n_Discarding entries that have BACends match coverage less than 96% and<br>_n_n_start/stop more than 20bp away from the BAC/PAC edge, 138,880 entries<br>_n_n_are left.  In these, the percent identity of the matching blocks is<br>_n_n_distributed as follows:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_88_t_t__t_t_169<br>_n_n_89_t_t__t_t_1667<br>_n_n_90_t_t__t_t_3761<br>_n_n_91_t_t__t_t_5643<br>_n_n_92_t_t__t_t_6985<br>_n_n_93_t_t__t_t_7944<br>_n_n_94_t_t__t_t_9020<br>_n_n_95_t_t__t_t_17224<br>_n_n_96_t_t__t_t_19312<br>_n_n_97_t_t__t_t_18551<br>_n_n_98_t_t__t_t_19234<br>_n_n_99_t_t__t_t_20152<br>_n_n_100_t_t__t_t_9218<br>_n_n_<br>_n_n_<br>_n_n_Filtering out the matches with less than 97% identity leaves 67,155.<br>_n_n_<br>_n_n_Many of the BACends hit more than once.  The distribution of the hit<br>_n_n_frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_11686<br>_n_n_02_t_t__t_t_3287<br>_n_n_03_t_t__t_t_1129<br>_n_n_04_t_t__t_t_530<br>_n_n_05_t_t__t_t_243<br>_n_n_06_t_t__t_t_192<br>_n_n_07_t_t__t_t_210<br>_n_n_08_t_t__t_t_317<br>_n_n_09_t_t__t_t_161<br>_n_n_10_t_t__t_t_159<br>_n_n_20_t_t__t_t_493<br>_n_n_30_t_t__t_t_261<br>_n_n_40_t_t__t_t_147<br>_n_n_50_t_t__t_t_49<br>_n_n_60_t_t__t_t_29<br>_n_n_70_t_t__t_t_50<br>_n_n_80_t_t__t_t_31<br>_n_n_90_t_t__t_t_28<br>_n_n_&gt;90_t_t__t_t_44<br>_n_n_<br>_n_n_<br>_n_n_BACends that hit more than three times are removed, with 18,260 hits<br>_n_n_remaining.  These went into the Gramene Sequence Viewer.<br>_n_n_<br>_n_n_	0
vocabularysubmission	Controlled vocabulary online submission form	<br>(NB: the present ontology terms can be searched at <a target="external" href="/documentation/../plant_ontology/">http://www.gramene.org/plant_ontology/</a>_n_n_)</ul>_n_n_</ul>_n_n__n_n_<p><br><a name=reference><b>Reference for the new suggestion:</b></a>_n_n_<br>&nbsp;_n_n_<ul>_n_n_  _n_n_<li>_n_n_<a name=ref_category><b>Reference category</b></a><font color="#666600"><font size=+1>*</font></font><b>:</b>_n_n_mention the documentary evidence for the suggested term e.g. published_n_n_or a personal communication. The option "curator" is for internal use.</li>_n_n__n_n_<li>_n_n_<a name=curator><b>Curator:</b></a> do not select unless you have been authorized as a curator_n_n_by the Gramene</li>_n_n__n_n_<li>_n_n_<a name=ref_source><b>Ref. Source:</b></a> If the option "published" is selected in the "Reference_n_n_category", then select from the drop of menu, the source of publication,_n_n_whether it is</li>_n_n__n_n_<ul>_n_n_<li>_n_n_<u>PubMed:</u> if an article is available from PubMed</li>_n_n__n_n_<li>_n_n_<u>ISBN:</u> Mention the ISBN number of the publication, published Journal_n_n_(if not listed by PubMed) or Book. .</li>_n_n__n_n_<li>_n_n_<u>Web site:</u> if the information is presented on a web site, preferably_n_n_authored by a scientist or hosted by a scientific institution.</li>_n_n__n_n_<li>_n_n_<u>Database:</u> if the information is available from a scientific database_n_n_e.g. TAIR, SGD, MIPS, GenBank, EMBL, Expasy, etc.</li>_n_n__n_n_<li>_n_n_<u>Others</u>: Carefully select this option only if any of the above does not_n_n_apply.  This will help our curators in assertianing a quality check on your_n_n_contribution.</li>_n_n_</ul>_n_n__n_n_<li>_n_n_<a name=ref_details><b>Reference details:</b></a> please provide the complete citation for the_n_n_reference which should be referred for the suggested term.</li>_n_n_</ul>_n_n_</ul>_n_n_<a name=comments><b>Comments:</b></a> provide your comments (if any), which you think the curators_n_n_and users community should be informed about the suggested term._n_n_<p><a name=contributor><b>Contributor information:</b></a> the contributor should provide the correct_n_n_information about&nbsp; him/herself, to help us identify your contribution._n_n_Your valuable contribution will be cited, if found appropriate. The mandatory_n_n_(<font color="#666600"><b><font size=+1>*</font></b>)<font size=+1> </font></font>fields_n_n_are:_n_n_<blockquote>Last (Family) name_n_n_<br>First name_n_n_<br>Organization/institution_n_n_<br>Address_n_n_<br>City_n_n_<br>Country_n_n_<br>Email</blockquote>_n_n_<b>PDF version of the submission form:</b> In case the problem is incurred_n_n_in ONLINE submission, please print/save the <a target="external" href="/documentation/../plant_ontology/suggestions.pdf">PDF_n_n_version</a> _n_n_<br>(<a target="external" href="/documentation/../plant_ontology/suggestions.pdf">http://www.gramene.org/plant_ontology/suggestions.pdf</a>_n_n_) of this fill in (allows you to type in the fields) form and send in email/mail/fax at the following address._n_n_<br>_n_n_<blockquote>_n_n_Pankaj Jaiswal, Ph.D.<br>_n_n_G15 Bradfield Hall<br>_n_n_Department of Plant Breeding<br>_n_n_Cornell University<br>_n_n_Ithaca, NY 14853<br>_n_n_U.S.A.<br>_n_n_<br>_n_n_TEL: +1-607-255-3103<br>_n_n_FAX: +1-607-255-6683<br>_n_n_Email: <a target="external" href="mailto:pj37@cornell.edu">pj37@cornell.edu</a><br>_n_n_</blockquote>_n_n__n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_<br>&nbsp;_n_n_	1
cornell_ssr	Positioning Cornell Rice SSRs on the Rice Genome.	/*<br>_n_n_This documents the processing of BAC-SSR alignments for CU-SSRs<br>_n_n_Lenny Teytelman<br>_n_n_April 6, 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The 1,847 BACs/PACs are from the GenBenk Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot;.<br>_n_n_<br>_n_n_The 524 CU SSRs are from www.gramene.org.  Only 499 of the SSRs had<br>_n_n_primers.<br>_n_n_<br>_n_n_The SSRs and BACs where aligned using e-PCR.  e-PCR was run with default<br>_n_n_settings of 50-bp margin and 0 allowed mismatches.  This resulted in<br>_n_n_297 matches, from 228 SSRs to 246 sequenced clones.<br>_n_n_	0
bac_marker	Mapping JRGP/Cornell Markers onto the Rice Genome	/*<br>_n_n_This documents the processing of Cornell and JRGP oryza sativa genetic<br>_n_n_markers to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Sun Mar 24 20:22:26 2002<br>_n_n_*/<br>_n_n_<br>_n_n_<br>_n_n_The Bacs are from the GenBenk Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The genetic markers are from the Cornell and JRGP genetic maps.  Using<br>_n_n_accessions of the markers, sequences were retrieved for each marker<br>_n_n_from GenBank.<br>_n_n_<br>_n_n_1,847 sequences were compared to  3,965 marker sequences from a total of<br>_n_n_2,682 genetic markers, using BLAT with -minScore=120.   The BLAT results<br>_n_n_contained 4,753 alignments.<br>_n_n_<br>_n_n_For the genomic markers, the distribution of the sequenced clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length        Count<br>_n_n_------        ----------<br>_n_n_&lt;010_t_t__t_t_339<br>_n_n_&lt;020_t_t__t_t_33<br>_n_n_&lt;030_t_t__t_t_15<br>_n_n_&lt;040_t_t__t_t_8<br>_n_n_&lt;050_t_t__t_t_3<br>_n_n_&lt;060_t_t__t_t_6<br>_n_n_&lt;070_t_t__t_t_5<br>_n_n_&lt;090_t_t__t_t_1<br>_n_n_&lt;200_t_t__t_t_3<br>_n_n_&lt;300_t_t__t_t_8<br>_n_n_&lt;400_t_t__t_t_2<br>_n_n_&lt;500_t_t__t_t_4<br>_n_n_&lt;800_t_t__t_t_1<br>_n_n_&gt;900_t_t__t_t_8<br>_n_n_<br>_n_n_<br>_n_n_For the cDNA markers, the distribution of BAC gap lengths is:<br>_n_n_Bac Gap<br>_n_n_Length_t_t_      Count<br>_n_n_------_t_t_      ----------<br>_n_n_&lt;010_t_t__t_t_2059<br>_n_n_&lt;020_t_t__t_t_121<br>_n_n_&lt;030_t_t__t_t_50<br>_n_n_&lt;040_t_t__t_t_37<br>_n_n_&lt;050_t_t__t_t_17<br>_n_n_&lt;060_t_t__t_t_14<br>_n_n_&lt;070_t_t__t_t_18<br>_n_n_&lt;080_t_t__t_t_52<br>_n_n_&lt;090_t_t__t_t_79<br>_n_n_&lt;100_t_t__t_t_95<br>_n_n_&lt;200_t_t__t_t_296<br>_n_n_&lt;300_t_t__t_t_226<br>_n_n_&lt;400_t_t__t_t_163<br>_n_n_&lt;500_t_t__t_t_121<br>_n_n_&lt;600_t_t__t_t_94<br>_n_n_&lt;700_t_t__t_t_73<br>_n_n_&lt;800_t_t__t_t_80<br>_n_n_&lt;900_t_t__t_t_64<br>_n_n_&gt;900_t_t__t_t_511<br>_n_n_<br>_n_n_<br>_n_n_In the case of genomic markers, the true hits should not have large<br>_n_n_gaps just as for BACend to BAC alignments.  And similarly to BACends,<br>_n_n_genomic markers aligning with a gap of greater than 20bp were discarded.<br>_n_n_For cDNA markers, hits with gaps greater that 3000 bp were filtered out.<br>_n_n_This left 4,677 hits.<br>_n_n_<br>_n_n_For a true match, the match should extend over most of the marker length.<br>_n_n_The following is the distribution of the percentages of match legths<br>_n_n_relative to total marker length:<br>_n_n_<br>_n_n_% of Marker<br>_n_n_matched    Count<br>_n_n_--------   ------<br>_n_n_=100_t_t__t_t_262<br>_n_n_99_t_t__t_t_383<br>_n_n_98_t_t__t_t_293<br>_n_n_97_t_t__t_t_277<br>_n_n_96_t_t__t_t_379<br>_n_n_95_t_t__t_t_344<br>_n_n_94_t_t__t_t_266<br>_n_n_93_t_t__t_t_173<br>_n_n_92_t_t__t_t_167<br>_n_n_91_t_t__t_t_122<br>_n_n_90_t_t__t_t_108<br>_n_n_85-89_t_t__t_t_263<br>_n_n_80-84_t_t__t_t_187<br>_n_n_70-79_t_t__t_t_264<br>_n_n_60-69_t_t__t_t_194<br>_n_n_50-59_t_t__t_t_178<br>_n_n_40-49_t_t__t_t_135<br>_n_n_30-39_t_t__t_t_121<br>_n_n_20-29_t_t__t_t_340<br>_n_n_10-19_t_t__t_t_218<br>_n_n_0-9_t_t__t_t_2<br>_n_n_<br>_n_n_<br>_n_n_Deleting the matches that cover less than 90% of the marker results in<br>_n_n_2,775 hits. The percent identity for the remaining matches is:<br>_n_n_<br>_n_n_Percent<br>_n_n_Identity_t_t_Count<br>_n_n_---------- ----------<br>_n_n_95_t_t__t_t_2<br>_n_n_96_t_t__t_t_14<br>_n_n_97_t_t__t_t_38<br>_n_n_98_t_t__t_t_183<br>_n_n_99_t_t__t_t_1081<br>_n_n_100_t_t__t_t_1457<br>_n_n_<br>_n_n_<br>_n_n_Of the above matches, 2,531 are from markers that align to a BAC from<br>_n_n_the same chromosome as indicated on the marker map.  These hits represent<br>_n_n_1,320 markers on 1,062 sequenced clones and they went into the Sequence<br>_n_n_Viewer.<br>_n_n_<br>_n_n_	0
marker_marker	Establishing Marker-Marker Correspondences for JRGP and Cornell Rice Genetic Markers	Establishing Marker-Marker Correspondences for JRGP and Cornell Rice<br>_n_n_Genetic Markers<br>_n_n_<br>_n_n_The markers consist of JRGP2000 map study markers<br>_n_n_from(http://rgp.dna.affrc.go.jp/publicdata/geneticmap2000/index.html)<br>_n_n_and the RG/RZ markers from the Gramen Cornell Rice Consensus<br>_n_n_(http://www.gramene.org/gramene/map/table?class=Map).<br>_n_n_<br>_n_n_Out of 3,267 JRGP and 378 Cornell markers, 2,845 have sequences in<br>_n_n_GenBank. Many of the markers have a 3' and a 5' accession or an older<br>_n_n_version of the sequence.  And 318 markers are multi-hybridizing markers<br>_n_n_that are known to hybridize to multiple locations.  They are deposited in<br>_n_n_GenBank under the same accession and usually have A/B/C... suffix after<br>_n_n_the marker name.  So in all, 4,205 sequences representing the  markers<br>_n_n_were downloaded.<br>_n_n_<br>_n_n_The JRGP markers contain 800 markers without a listed accession marker.<br>_n_n_A total of 1,374 genomic and 1,893 cDNA markers are in the JRGP map study.<br>_n_n_In the Cornell Rice Consensus, 164 markers are genomic and 214 are cDNAs.<br>_n_n_<br>_n_n_Blatting the file containing the sequences against itself results in<br>_n_n_5,316 matches with minScore=120.  Most of these are self-alignments for<br>_n_n_each of the sequences.  Deleting these leaves 689 entries.<br>_n_n_<br>_n_n_If accessions A and B align, there will be most of the time two entries<br>_n_n_in the blat results: A-&gt;B and B-&gt;A.  Removing the second of the two<br>_n_n_matches leaves 362 matches that contain a total of 352 markers.<br>_n_n_<br>_n_n_Of the 362 matches, 113 are Cornell-JRGP hits; 31 are Cornell-Cornell,<br>_n_n_and 218 are JRGP-JRGP matches.  The 362 matches represent 279 unique<br>_n_n_marker-to-marker correspondences.<br>_n_n_<br>_n_n_Of the 352 markers, 49 are the multi-hybridizing ones.  Exluding these,<br>_n_n_marker correspondencess that from different chromosomes or are more than<br>_n_n_30cM apart are flagged as discordant.  A total of 153  correspondences<br>_n_n_fall into the discordant category.<br>_n_n_<br>_n_n_The 126 concordant correspondences went into the Map Viewer.<br>_n_n_<br>_n_n_September 10, 2001<br>_n_n_	0
oryza_cds	Aligning Oryza Sativa(Rice) CDSs onto the Rice Genome	/*<br>_n_n_This documents the processing of oryza sativa CDSs to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Fri Apr 26 00:18:05 2002<br>_n_n_*/<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The Oryza Sativa coding sequences are from the GenBank Entrez<br>_n_n_nucleotide query: &quot;(txid4530[ORGN] AND complete[TITL] AND cds[TITL])<br>_n_n_NOT (Mitochondrion[ALL] OR Chloroplast[ALL] OR Mitochondrial[ALL]) )<br>_n_n_&quot;  The average CDSs length is 2,091.<br>_n_n_<br>_n_n_<br>_n_n_1,858 sequences were compared to  1,358 CDSs using BLAT with minScore=120.<br>_n_n_The 28,064 BLAT hits were filtered using pslReps utility.  This resulted<br>_n_n_in 1,790 alignments.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_True hits should extend over all of the CDSs, unless the hit is at the<br>_n_n_very end or beginning of a BAC/PAC. The following is the distribution<br>_n_n_of the percentage coverage for the CDSs:<br>_n_n_<br>_n_n_% of CDSs<br>_n_n_matched_t_t__t_t_    Count<br>_n_n_--------_t_t_    ------<br>_n_n_0-9_t_t__t_t_237<br>_n_n_10-19_t_t__t_t_36<br>_n_n_20-29_t_t__t_t_71<br>_n_n_30-39_t_t__t_t_16<br>_n_n_40-49_t_t__t_t_12<br>_n_n_50-59_t_t__t_t_11<br>_n_n_60-69_t_t__t_t_27<br>_n_n_70-79_t_t__t_t_31<br>_n_n_80-84_t_t__t_t_29<br>_n_n_85-89_t_t__t_t_22<br>_n_n_90_t_t__t_t_8<br>_n_n_91_t_t__t_t_9<br>_n_n_92_t_t__t_t_13<br>_n_n_93_t_t__t_t_6<br>_n_n_94_t_t__t_t_45<br>_n_n_95_t_t__t_t_82<br>_n_n_96_t_t__t_t_25<br>_n_n_97_t_t__t_t_40<br>_n_n_98_t_t__t_t_72<br>_n_n_99_t_t__t_t_349<br>_n_n_=100_t_t__t_t_195<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Discarding the hits that cover less than 96 percent of the CDSs  and<br>_n_n_start/stop more than 20bp away from the BAC/PAC edge leaves 803 hits.<br>_n_n_These have the following BAC gaps:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_   Count<br>_n_n_------ ----------<br>_n_n_01000_t_t__t_t_517<br>_n_n_02000_t_t__t_t_129<br>_n_n_03000_t_t__t_t_73<br>_n_n_04000_t_t__t_t_30<br>_n_n_05000_t_t__t_t_21<br>_n_n_06000_t_t__t_t_11<br>_n_n_07000_t_t__t_t_3<br>_n_n_08000_t_t__t_t_2<br>_n_n_09000_t_t__t_t_7<br>_n_n_10000_t_t__t_t_3<br>_n_n_20000_t_t__t_t_5<br>_n_n_30000_t_t__t_t_2<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_For the sake of clean displays, the hits with gaps greater than 3,000<br>_n_n_are removed.  This results in 719 entries.  The percent identity for<br>_n_n_the remaining matches is:<br>_n_n_<br>_n_n_Percent<br>_n_n_Identity_t_t_Count<br>_n_n_---------- ----------<br>_n_n_92_t_t__t_t_1<br>_n_n_94_t_t__t_t_1<br>_n_n_95_t_t__t_t_3<br>_n_n_96_t_t__t_t_64<br>_n_n_97_t_t__t_t_21<br>_n_n_98_t_t__t_t_48<br>_n_n_99_t_t__t_t_344<br>_n_n_100_t_t__t_t_237<br>_n_n_<br>_n_n_<br>_n_n_Some of the CDSs hit more than once.  The distribution of the hits is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_CDSs_t_t_  # of EST<br>_n_n_---_t_t_-----<br>_n_n_01_t_t__t_t_374<br>_n_n_02_t_t__t_t_108<br>_n_n_03_t_t__t_t_20<br>_n_n_04_t_t__t_t_1<br>_n_n_05_t_t__t_t_1<br>_n_n_70_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 505 unique CDSs and 413 sequenced clones.  Those having<br>_n_n_at least one gap of length 50 or above, are considered multi-exon<br>_n_n_CDSs hits.  287 are multi-exon and 220 are single-exon hits.<br>_n_n_<br>_n_n_	0
bicolor_est	Aligning Sorghum Bicolor ESTs onto the Rice Genome	/*<br>_n_n_This documents the processing of sorghum bicolor ESTs to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Mon Mar 25 12:40:01 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The ESTs are from the GenBank nucleotide query &quot;txid4558[orgn]  AND<br>_n_n_gbdiv_est[PROP]&quot;  The average ESTs length is 475.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_1,847 sequences were compared to  84,711 ESTs using BLAT with<br>_n_n_mindIdentity=50.   The 130,295 BLAT hits were filtered using pslReps<br>_n_n_utility with -minAli=0.85 -nearTop=0.01.  This resulted in 68,126<br>_n_n_alignments.<br>_n_n_<br>_n_n_The lengths of the matches are distributed as follows:<br>_n_n_<br>_n_n_Length of<br>_n_n_hits_t_t_     Count<br>_n_n_--------     ------<br>_n_n_0-100_t_t__t_t_13040<br>_n_n_100-150_t_t__t_t_8259<br>_n_n_150-200_t_t__t_t_8372<br>_n_n_200-250_t_t__t_t_7866<br>_n_n_250-300_t_t__t_t_7945<br>_n_n_300-350_t_t__t_t_7464<br>_n_n_350-400_t_t__t_t_6186<br>_n_n_400-450_t_t__t_t_4337<br>_n_n_450-500_t_t__t_t_2527<br>_n_n_500-550_t_t__t_t_1400<br>_n_n_550-600_t_t__t_t_500<br>_n_n_600-650_t_t__t_t_177<br>_n_n_650-700_t_t__t_t_42<br>_n_n_700-750_t_t__t_t_2<br>_n_n_750-800_t_t__t_t_4<br>_n_n_&gt;800_t_t__t_t_5<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Removing matches with less than 150bp match-length leaves 46,660 hits.<br>_n_n_<br>_n_n_Many of the ESTs hit more than once.  The distribution of the hit<br>_n_n_frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_17961<br>_n_n_02_t_t__t_t_7662<br>_n_n_03_t_t__t_t_2421<br>_n_n_04_t_t__t_t_442<br>_n_n_05_t_t__t_t_221<br>_n_n_06_t_t__t_t_239<br>_n_n_07_t_t__t_t_204<br>_n_n_08_t_t__t_t_33<br>_n_n_09_t_t__t_t_3<br>_n_n_10_t_t__t_t_6<br>_n_n_20_t_t__t_t_2<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_ESTs that hit more than three times are removed, with 40,548 hits<br>_n_n_remaining.  These matches have the following distribution of the percent<br>_n_n_identity per hit:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_82_t_t__t_t_507<br>_n_n_83_t_t__t_t_1296<br>_n_n_84_t_t__t_t_1824<br>_n_n_85_t_t__t_t_2652<br>_n_n_86_t_t__t_t_3175<br>_n_n_87_t_t__t_t_4008<br>_n_n_88_t_t__t_t_4402<br>_n_n_89_t_t__t_t_4842<br>_n_n_90_t_t__t_t_4934<br>_n_n_91_t_t__t_t_4484<br>_n_n_92_t_t__t_t_3142<br>_n_n_93_t_t__t_t_1889<br>_n_n_94_t_t__t_t_1225<br>_n_n_95_t_t__t_t_1139<br>_n_n_96_t_t__t_t_479<br>_n_n_97_t_t__t_t_154<br>_n_n_98_t_t__t_t_107<br>_n_n_99_t_t__t_t_230<br>_n_n_100_t_t__t_t_59<br>_n_n_<br>_n_n_<br>_n_n_The distribution of the sequenced clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_      Count<br>_n_n_------_t_t_      ----------<br>_n_n_01000_t_t__t_t_35394<br>_n_n_02000_t_t__t_t_3717<br>_n_n_03000_t_t__t_t_683<br>_n_n_04000_t_t__t_t_241<br>_n_n_05000_t_t__t_t_110<br>_n_n_06000_t_t__t_t_73<br>_n_n_07000_t_t__t_t_36<br>_n_n_08000_t_t__t_t_10<br>_n_n_09000_t_t__t_t_19<br>_n_n_10000_t_t__t_t_14<br>_n_n_20000_t_t__t_t_126<br>_n_n_30000_t_t__t_t_57<br>_n_n_40000_t_t__t_t_42<br>_n_n_50000_t_t__t_t_9<br>_n_n_60000_t_t__t_t_10<br>_n_n_70000_t_t__t_t_3<br>_n_n_80000_t_t__t_t_3<br>_n_n_&gt;90000_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 28,044 unique ESTs and 1,634 sequenced clones.<br>_n_n_Those having at least one gap of length 50 or above, are considered<br>_n_n_multi-exon hits.  21,150 are multi-exon and 8,020 are single-exon hits.<br>_n_n_<br>_n_n_	0
vocabulary	Controlled Vocabulary Database	<br><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; %male fertility_n_n_restoration trait ; TO:0000308 % hybrid evaluation ; TO:0000334</font>_n_n_<br><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp; %incompatibility trait ; TO:0000035</font>_n_n_<br><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; %hybrid incompatibilty_n_n_; TO:0000036</font>_n_n_<br><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; %self-incompatibility_n_n_trait ; TO:0000310</font>_n_n_<br><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp; %sterility related trait ; TO:0000485</font>_n_n_<br><font size=-1>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; %female sterility_n_n_trait ; TO:0000358</font></blockquote>_n_n__n_n_<p><br><font face="Arial,Helvetica"><font size=-1>Note that terms may have_n_n_more than one parent, and may (obviously) have zero or more children. However,_n_n_currently there are no links between the TO and the three sub-ontologies_n_n_within GO. You can click on any of the terms in these lists to make the_n_n_clicked term the current one for display.</font></font>_n_n_<p><b><font face="Arial,Helvetica">Mutant/Protein Associations<font size=-1>:</font></font></b><font face="Arial,Helvetica"><font size=-1>_n_n_Common Concurrent Assignments</font></font>_n_n_<br><font face="Arial,Helvetica"><font size=-1>This section, if present,_n_n_contains a list of TO/GO terms that are, statistically speaking,&nbsp;_n_n_commonly assigned to the mutants or proteins along with the currently displayed_n_n_term. For example, "hydrogen transport (<a target="external" href="/perl/ontology/search_term?id=GO:0006818">GO:0006818</a>)"_n_n_is mapped by various methods to approximately 19 proteins from rice&nbsp;_n_n_but 4 of such proteins from rice are also mapped to the "P-type ATPase_n_n_(<a target="external" href="/perl/ontology/search_term?id=GO:0015662">GO:0015662</a>)"._n_n_This display allows you to investigate potential conceptual linkages between_n_n_otherwise unrelated GO terms on the basis of their common assignment to_n_n_sets&nbsp; of proteins. This is just an example with the GO term, in future_n_n_we will provide the similar examples for the mutants and phenotypes associated_n_n_with the TO as well as GO terms.</font></font>_n_n_<p><b>Evidence codes:</b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>The database supports each assertion of_n_n_phenotypic or the&nbsp; protein information from rice by evidence codes,_n_n_that describes the basis for the assertion of either the TO or the GO_n_n_components. The table of evidence codes used by Gramene is available_n_n_<a target="external" href="/plant_ontology/evidence_codes.html">here</a></font></font>._n_n_<p><b><font face="Arial,Helvetica">Links to Ontology flat files:</font></b>_n_n_<p><font size=-1>The flat files for the TO / GO&nbsp; terms and definitions_n_n_can be downloaded from the following sites and can be browsed by using_n_n_the stand-alone <a target="external" href="http://www.godatabase.org/dev/editor.html">Browser</a></font>_n_n_<p><font size=-1>Trait Ontology<sup>TM</sup> for Rice:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_n_n__n_n_<a target="external" href="/plant_ontology/trait.ontology">Trait_n_n_terms</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_n_n__n_n_<a target="external" href="/plant_ontology/trait.definition">Definitions&nbsp;</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_n_n__n_n_<a target="external" href="/plant_ontology/traits.zip">Trait.zip_n_n_File</a></font>_n_n_<p><font size=-1>Gene Ontology<sup>TM</sup>:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;_n_n__n_n_<a target="external" href="ftp://ftp.geneontology.org/pub/go/ontology/function.ontology">Molecular_n_n_function</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a target="external" href="ftp://ftp.geneontology.org/pub/go/ontology/process.ontology">Biological_n_n_process&nbsp;</a>&nbsp;&nbsp;&nbsp;&nbsp; <a target="external" href="ftp://ftp.geneontology.org/pub/go/ontology/component.ontology">Cellular_n_n_	2
vocabulary	Controlled Vocabulary Database	component</a>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a target="external" href="http://www.geneontology.org/doc/GO.doc.html">General Documentation</a></font>_n_n_<p><b><font face="Arial,Helvetica">Suggestions/Corrections:</font></b>_n_n_<br><font face="Arial,Helvetica"><font size=-1>If you would like to make_n_n_any suggestion for the new term/definition/update/correction to an existing_n_n_term, please use the <a target="external" href="/plant_ontology/submission">ONLINE_n_n_submission form</a> for the purpose. We appreciate your valuable feedback on_n_n_our efforts. Needless to mention your contribution will be duly acknowledged.</font></font>_n_n_<p><font size=-1>For more details on the Gene Ontology terms please refer_n_n_to <a target="external" href="http://www.geneontology.org">www.geneontology.org</a></font>_n_n_	3
IRGSP	Aligning IRGSP Oryza Sativa(Rice) ESTs onto the Rice Genome	/*<br>_n_n_This documents the processing of Oryza Sativa BAC-EST alignments<br>_n_n_Lenny Teytelman<br>_n_n_Tue Apr  2 08:53:38 2002<br>_n_n_*/<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The ESTs are from the Genbank Entrez Nucleotide query &quot;txid4530[orgn]<br>_n_n_AND  gbdiv_est[PROP]&quot;.  The average EST length is 367.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_1,847 sequences were compared to  104,549 ESTs using BLAT with<br>_n_n_minScore=120.   The 173,370 BLAT hits were filtered using pslReps utility.<br>_n_n_This resulted in 103,766 alignments.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_True hits should extend over all of the est, unless the hit is at the<br>_n_n_very end or beginning of a BAC/PAC. The following is the distribution<br>_n_n_of the percentage coverage for the ests:<br>_n_n_<br>_n_n_% of EST<br>_n_n_matched    Count<br>_n_n_--------   ------<br>_n_n_10-19_t_t__t_t_37<br>_n_n_20-29_t_t__t_t_1093<br>_n_n_30-39_t_t__t_t_3387<br>_n_n_40-49_t_t__t_t_6760<br>_n_n_50-59_t_t__t_t_3070<br>_n_n_60-69_t_t__t_t_2683<br>_n_n_70-79_t_t__t_t_3030<br>_n_n_80-84_t_t__t_t_2443<br>_n_n_85-89_t_t__t_t_3728<br>_n_n_90_t_t__t_t_1123<br>_n_n_91_t_t__t_t_1374<br>_n_n_92_t_t__t_t_1688<br>_n_n_93_t_t__t_t_2205<br>_n_n_94_t_t__t_t_3336<br>_n_n_95_t_t__t_t_4430<br>_n_n_96_t_t__t_t_6327<br>_n_n_97_t_t__t_t_9403<br>_n_n_98_t_t__t_t_15082<br>_n_n_99_t_t__t_t_20489<br>_n_n_=100_t_t__t_t_12078<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Discarding the hits that cover less than 96 percent of the ESTs  and<br>_n_n_start/stop more than 20bp away from the BAC/PAC edge leaves 68,938 hits.<br>_n_n_These have the following BAC gaps:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_   Count<br>_n_n_------ ----------<br>_n_n_01000_t_t__t_t_61356<br>_n_n_02000_t_t__t_t_5799<br>_n_n_03000_t_t__t_t_1207<br>_n_n_04000_t_t__t_t_272<br>_n_n_05000_t_t__t_t_137<br>_n_n_06000_t_t__t_t_39<br>_n_n_07000_t_t__t_t_50<br>_n_n_08000_t_t__t_t_13<br>_n_n_09000_t_t__t_t_10<br>_n_n_10000_t_t__t_t_7<br>_n_n_20000_t_t__t_t_27<br>_n_n_30000_t_t__t_t_9<br>_n_n_40000_t_t__t_t_4<br>_n_n_50000_t_t__t_t_4<br>_n_n_60000_t_t__t_t_2<br>_n_n_&gt;90000_t_t__t_t_2<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_For the sake of clean displays, the hits with gaps greater than 3,000<br>_n_n_are removed.  This results in 68,362 entries.  The percent identity for<br>_n_n_the remaining matches is:<br>_n_n_<br>_n_n_Percent<br>_n_n_Identity_t_t_Count<br>_n_n_---------- ----------<br>_n_n_92_t_t__t_t_1<br>_n_n_94_t_t__t_t_20<br>_n_n_95_t_t__t_t_136<br>_n_n_96_t_t__t_t_571<br>_n_n_97_t_t__t_t_1899<br>_n_n_98_t_t__t_t_6785<br>_n_n_99_t_t__t_t_24088<br>_n_n_100_t_t__t_t_34862<br>_n_n_<br>_n_n_<br>_n_n_Some of the ESTs hit more than once.  The distribution of the hits is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_EST_t_t_  # of EST<br>_n_n_---_t_t_-----<br>_n_n_01_t_t__t_t_35605<br>_n_n_02_t_t__t_t_12433<br>_n_n_03_t_t__t_t_1174<br>_n_n_04_t_t__t_t_197<br>_n_n_05_t_t__t_t_55<br>_n_n_06_t_t__t_t_118<br>_n_n_07_t_t__t_t_123<br>_n_n_08_t_t__t_t_14<br>_n_n_09_t_t__t_t_5<br>_n_n_10_t_t__t_t_2<br>_n_n_20_t_t__t_t_21<br>_n_n_30_t_t__t_t_8<br>_n_n_40_t_t__t_t_5<br>_n_n_50_t_t__t_t_2<br>_n_n_60_t_t__t_t_6<br>_n_n_70_t_t__t_t_1<br>_n_n_&gt;90_t_t__t_t_4<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 49,773 unique ESTs and 1,821 sequenced clones.  Those<br>_n_n_having at least one gap of length 50 or above, are considered multi-exon<br>_n_n_est hits.  21,707 are multi-exon and 28,106 are single-exon hits.<br>_n_n_<br>_n_n_The above hits went into the Sequence Viewer as two separate tracks.<br>_n_n_	0
indica_est	Aligning BGI Oryza Sativa(Rice) Indica ESTs onto the Rice Genome	/*<br>_n_n_This documents the processing of oryza sativa ESTs to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Fri Apr 19 13:26:09 2002<br>_n_n_*/<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_The ESTs are from BGI,http://btn.genomics.org.cn/rice/.  For each EST,<br>_n_n_15bp have been removed from the front and 50bp from the back.  The average<br>_n_n_ESTs length is 417.<br>_n_n_<br>_n_n_<br>_n_n_1,858 sequences were compared to  86,623 ESTs using BLAT with<br>_n_n_minScore=120.   The 120,872 BLAT hits were filtered using pslReps utility.<br>_n_n_This resulted in 80,156 alignments.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_True hits should extend over all of the ESTs, unless the hit is at the<br>_n_n_very end or beginning of a BAC/PAC. The following is the distribution<br>_n_n_of the percentage coverage for the ESTs:<br>_n_n_<br>_n_n_% of ESTs<br>_n_n_matched_t_t__t_t_    Count<br>_n_n_--------_t_t_    ------<br>_n_n_10-19_t_t__t_t_1<br>_n_n_20-29_t_t__t_t_406<br>_n_n_30-39_t_t__t_t_1158<br>_n_n_40-49_t_t__t_t_1258<br>_n_n_50-59_t_t__t_t_1244<br>_n_n_60-69_t_t__t_t_1347<br>_n_n_70-79_t_t__t_t_2464<br>_n_n_80-84_t_t__t_t_2491<br>_n_n_85-89_t_t__t_t_4272<br>_n_n_90_t_t__t_t_1325<br>_n_n_91_t_t__t_t_1567<br>_n_n_92_t_t__t_t_2086<br>_n_n_93_t_t__t_t_2790<br>_n_n_94_t_t__t_t_3330<br>_n_n_95_t_t__t_t_4298<br>_n_n_96_t_t__t_t_5143<br>_n_n_97_t_t__t_t_6570<br>_n_n_98_t_t__t_t_11383<br>_n_n_99_t_t__t_t_18952<br>_n_n_=100_t_t__t_t_8071<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Discarding the hits that cover less than 96 percent of the ESTs  and<br>_n_n_start/stop more than 20bp away from the BAC/PAC edge leaves 55,483 hits.<br>_n_n_These have the following BAC gaps:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_   Count<br>_n_n_------ ----------<br>_n_n_01000_t_t__t_t_44913<br>_n_n_02000_t_t__t_t_7839<br>_n_n_03000_t_t__t_t_1731<br>_n_n_04000_t_t__t_t_561<br>_n_n_05000_t_t__t_t_160<br>_n_n_06000_t_t__t_t_81<br>_n_n_07000_t_t__t_t_66<br>_n_n_08000_t_t__t_t_41<br>_n_n_09000_t_t__t_t_29<br>_n_n_10000_t_t__t_t_13<br>_n_n_20000_t_t__t_t_43<br>_n_n_30000_t_t__t_t_5<br>_n_n_40000_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_For the sake of clean displays, the hits with gaps greater than 3,000<br>_n_n_are removed.  This results in 54,483 entries.  The percent identity for<br>_n_n_the remaining matches is:<br>_n_n_<br>_n_n_Percent<br>_n_n_Identity_t_t_Count<br>_n_n_---------- ----------<br>_n_n_93_t_t__t_t_4<br>_n_n_94_t_t__t_t_18<br>_n_n_95_t_t__t_t_130<br>_n_n_96_t_t__t_t_363<br>_n_n_97_t_t__t_t_1273<br>_n_n_98_t_t__t_t_6139<br>_n_n_99_t_t__t_t_29087<br>_n_n_100_t_t__t_t_17469<br>_n_n_<br>_n_n_<br>_n_n_Some of the ESTs hit more than once.  The distribution of the hits is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_ESTs_t_t_  # of EST<br>_n_n_---_t_t_-----<br>_n_n_01_t_t__t_t_29092<br>_n_n_02_t_t__t_t_9410<br>_n_n_03_t_t__t_t_1065<br>_n_n_04_t_t__t_t_116<br>_n_n_05_t_t__t_t_29<br>_n_n_06_t_t__t_t_64<br>_n_n_07_t_t__t_t_203<br>_n_n_08_t_t__t_t_15<br>_n_n_09_t_t__t_t_3<br>_n_n_10_t_t__t_t_4<br>_n_n_20_t_t__t_t_44<br>_n_n_30_t_t__t_t_2<br>_n_n_60_t_t__t_t_1<br>_n_n_&gt;90_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 40,049 unique ESTs and 1,810 sequenced clones.  Those<br>_n_n_having at least one gap of length 50 or above, are considered multi-exon<br>_n_n_ESTs hits.  23,692 are multi-exon and 16,383 are single-exon hits.<br>_n_n_<br>_n_n_	0
tigr_oryza	Aligning TIGR Oryza Sativa (Rice) Gene Index onto the Rice Genome	/*<br>_n_n_This documents the processing of oryza sativa TCs to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Fri Apr 26 02:48:25 2002<br>_n_n_*/<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_TIGR Maize Gene Index(ZmGI) is from http://www.tigr.org/tdb/ogi/  The<br>_n_n_average TCs length is 850.<br>_n_n_<br>_n_n_<br>_n_n_1,858 sequences were compared to  12,354 TCs using BLAT with<br>_n_n_minScore=120.   The 56,146 BLAT hits were filtered using pslReps<br>_n_n_utility.  This resulted in 12,971 alignments.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_True hits should extend over all of the TCs, unless the hit is at the<br>_n_n_very end or beginning of a BAC/PAC. The following is the distribution<br>_n_n_of the percentage coverage for the TCs:<br>_n_n_<br>_n_n_% of TCs<br>_n_n_matched             Count<br>_n_n_--------            ------<br>_n_n_0-9             25<br>_n_n_10-19           101<br>_n_n_20-29           106<br>_n_n_30-39           130<br>_n_n_40-49           117<br>_n_n_50-59           176<br>_n_n_60-69           257<br>_n_n_70-79           331<br>_n_n_80-84           217<br>_n_n_85-89           408<br>_n_n_90              130<br>_n_n_91              140<br>_n_n_92              163<br>_n_n_93              250<br>_n_n_94              332<br>_n_n_95              470<br>_n_n_96              870<br>_n_n_97              1077<br>_n_n_98              1752<br>_n_n_99              3664<br>_n_n_=100            2255<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Discarding the hits that cover less than 96 percent of the TCs  and<br>_n_n_start/stop more than 20bp away from the BAC/PAC edge leaves 10,194<br>_n_n_hits.  These have the following BAC gaps:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length     Count<br>_n_n_------ ----------<br>_n_n_01000           6769<br>_n_n_02000           1701<br>_n_n_03000           922<br>_n_n_04000           358<br>_n_n_05000           182<br>_n_n_06000           86<br>_n_n_07000           55<br>_n_n_08000           34<br>_n_n_09000           24<br>_n_n_10000           12<br>_n_n_20000           44<br>_n_n_30000           3<br>_n_n_40000           1<br>_n_n_50000           2<br>_n_n_&gt;90000          1<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_For the sake of clean displays, the hits with gaps greater than 3,000<br>_n_n_are removed.  This results in 9,392 entries.  The percent identity for<br>_n_n_the remaining matches is:<br>_n_n_<br>_n_n_Percent<br>_n_n_Identity        Count<br>_n_n_---------- ----------<br>_n_n_93              1<br>_n_n_94              1<br>_n_n_95              9<br>_n_n_96              47<br>_n_n_97              283<br>_n_n_98              691<br>_n_n_99              4285<br>_n_n_100             4075<br>_n_n_<br>_n_n_<br>_n_n_Some of the TCs hit more than once.  The distribution of the hits is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_TCs       # of EST<br>_n_n_---     -----<br>_n_n_01              4221<br>_n_n_02              1778<br>_n_n_03              204<br>_n_n_04              28<br>_n_n_05              16<br>_n_n_06              4<br>_n_n_07              10<br>_n_n_08              5<br>_n_n_09              2<br>_n_n_10              3<br>_n_n_20              6<br>_n_n_30              5<br>_n_n_40              1<br>_n_n_50              2<br>_n_n_60              3<br>_n_n_70              1<br>_n_n_90              1<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 6,290 unique TCs and 1,730 sequenced clones.  Those<br>_n_n_having at least one gap of length 50 or above, are considered<br>_n_n_multi-exon TCs hits.  4,195 are multi-exon and 2,101 are single-exon<br>_n_n_hits.<br>_n_n_<br>_n_n_	0
tigr_mays	Aligning TIGR Zea Mays (Maize) Gene Index onto the Rice Genome	/*<br>_n_n_This documents the processing of zea mays TCs and ESTs to the rice genome.<br>_n_n_Lenny Teytelman<br>_n_n_Mon Mar 25 14:23:35 2002<br>_n_n_*/<br>_n_n_<br>_n_n_The BACs/PACs are from the GenBank Entrez Nucleotide query:<br>_n_n_<br>_n_n_&quot;Oryza [ORGN] AND (30000 [SLEN]:250000 [SLEN]) AND ((htg [KYWD] OR BAC<br>_n_n_[ALL] OR chromosome [TITL] OR PAC [ALL]) NOT (marker [TITL] OR cDNA<br>_n_n_[TITL] OR mRNA [TITL] OR RAPD [TITL] OR GSS [KYWD] OR telomere [TITL]<br>_n_n_OR protein[TITL]))&quot; for BACs, and<br>_n_n_<br>_n_n_TIGR Maize Gene Index(ZmGI) is from http://www.tigr.org/tdb/zmgi/  The<br>_n_n_average TCs and ESTs length is 613.<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_1,847 sequences were compared to  27,642 TCs and ESTs using BLAT with<br>_n_n_mindIdentity=50.   The 30,064 BLAT hits were filtered using pslReps<br>_n_n_utility with -minAli=0.85 -nearTop=0.01.  This resulted in 16,202<br>_n_n_alignments.<br>_n_n_<br>_n_n_The lengths of the matches are distributed as follows:<br>_n_n_<br>_n_n_Length of<br>_n_n_hits_t_t_     Count<br>_n_n_--------     ------<br>_n_n_0-100_t_t__t_t_3274<br>_n_n_100-150_t_t__t_t_2137<br>_n_n_150-200_t_t__t_t_1968<br>_n_n_200-250_t_t__t_t_1639<br>_n_n_250-300_t_t__t_t_1538<br>_n_n_300-350_t_t__t_t_1266<br>_n_n_350-400_t_t__t_t_1164<br>_n_n_400-450_t_t__t_t_752<br>_n_n_450-500_t_t__t_t_536<br>_n_n_500-550_t_t__t_t_371<br>_n_n_550-600_t_t__t_t_249<br>_n_n_600-650_t_t__t_t_203<br>_n_n_650-700_t_t__t_t_175<br>_n_n_700-750_t_t__t_t_129<br>_n_n_750-800_t_t__t_t_96<br>_n_n_&gt;800_t_t__t_t_705<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_Removing matches with less than 150bp match-length leaves 10,756 hits.<br>_n_n_<br>_n_n_Many of the TCs and ESTs hit more than once.  The distribution of the<br>_n_n_hit frequencies is:<br>_n_n_<br>_n_n_# Of<br>_n_n_Hits per<br>_n_n_Feature       Count<br>_n_n_-------       -----<br>_n_n_01_t_t__t_t_4729<br>_n_n_02_t_t__t_t_1778<br>_n_n_03_t_t__t_t_434<br>_n_n_04_t_t__t_t_106<br>_n_n_05_t_t__t_t_43<br>_n_n_06_t_t__t_t_22<br>_n_n_07_t_t__t_t_19<br>_n_n_08_t_t__t_t_7<br>_n_n_09_t_t__t_t_5<br>_n_n_10_t_t__t_t_2<br>_n_n_20_t_t__t_t_7<br>_n_n_30_t_t__t_t_1<br>_n_n_40_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_<br>_n_n_TCs and ESTs that hit more than three times are removed, with 9,587<br>_n_n_hits remaining.  These matches have the following distribution of the<br>_n_n_percent identity per hit:<br>_n_n_<br>_n_n_% Identity_t_t_ Count<br>_n_n_----------_t_t_ ----------<br>_n_n_82_t_t__t_t_100<br>_n_n_83_t_t__t_t_336<br>_n_n_84_t_t__t_t_570<br>_n_n_85_t_t__t_t_779<br>_n_n_86_t_t__t_t_904<br>_n_n_87_t_t__t_t_1118<br>_n_n_88_t_t__t_t_1206<br>_n_n_89_t_t__t_t_1220<br>_n_n_90_t_t__t_t_1078<br>_n_n_91_t_t__t_t_855<br>_n_n_92_t_t__t_t_580<br>_n_n_93_t_t__t_t_332<br>_n_n_94_t_t__t_t_250<br>_n_n_95_t_t__t_t_115<br>_n_n_96_t_t__t_t_69<br>_n_n_97_t_t__t_t_45<br>_n_n_98_t_t__t_t_18<br>_n_n_99_t_t__t_t_9<br>_n_n_100_t_t__t_t_3<br>_n_n_<br>_n_n_<br>_n_n_The distribution of the sequenced clone gaps is:<br>_n_n_<br>_n_n_Bac Gap<br>_n_n_Length_t_t_      Count<br>_n_n_------_t_t_      ----------<br>_n_n_01000_t_t__t_t_7201<br>_n_n_02000_t_t__t_t_1470<br>_n_n_03000_t_t__t_t_513<br>_n_n_04000_t_t__t_t_166<br>_n_n_05000_t_t__t_t_55<br>_n_n_06000_t_t__t_t_37<br>_n_n_07000_t_t__t_t_27<br>_n_n_08000_t_t__t_t_21<br>_n_n_09000_t_t__t_t_7<br>_n_n_10000_t_t__t_t_17<br>_n_n_20000_t_t__t_t_35<br>_n_n_30000_t_t__t_t_16<br>_n_n_40000_t_t__t_t_10<br>_n_n_50000_t_t__t_t_7<br>_n_n_60000_t_t__t_t_3<br>_n_n_70000_t_t__t_t_1<br>_n_n_&gt;90000_t_t__t_t_1<br>_n_n_<br>_n_n_<br>_n_n_The hits represent 6,941 unique TCs and ESTs and 1,576 sequenced clones.<br>_n_n_Those having at least one gap of length 50 or above, are considered<br>_n_n_multi-exon hits.  5,884 are multi-exon and 1,254 are single-exon hits.<br>_n_n_<br>_n_n_	0
vocabularysubmission	Controlled vocabulary online submission form	_n_n_<table border="0" cellspacing="0" cellpadding="0" width="100%" >_n_n_<tr>_n_n_<td class="submitsubheader">&nbsp; </td>_n_n_</tr>_n_n_<tr align="left">_n_n_<td class="submitsubheader">Please use <a target="external" href="/plant_ontology/submission">this form</a> to suggest new terms for the plant ontology vocabulary. You can also use this form to suggest corrections.  A confirmation email will be sent to you by our curators within two days.</td>_n_n_</tr>_n_n_</table>_n_n__n_n_<table border="0" cellspacing="0" cellpadding="5" width="100%" >_n_n_<tr>_n_n_<td colspan="2" class="submitsubheadersmall">_n_n_<b><em>Note: Fields with asterisks (*) are mandatory.</em></b>_n_n_</td>_n_n_</tr>_n_n__n_n_</table>_n_n__n_n_<p><a name=submission_type><b>Submission type</b></a><font color="#666600"><font size=+1>*</font></font><b>:</b>_n_n_the drop menu allows you to select on the type of submission you are about_n_n_to make._n_n_<ul>_n_n_<li>_n_n_<u>New term:</u> if the suggestion is for a new term</li>_n_n__n_n_<li>_n_n_<u>New suggestion for a relationship:</u> if you think that for a term,_n_n_there should be either a new relationship or an additional one to an existing_n_n_parent term. The DAG(Directed Acyclic Graphs) allows the terms to have multiple parent-child relationships_n_n_unless a cycle is created, which is not allowed.</li>_n_n__n_n_<li>_n_n_<u>Correction:</u> suggest for mistakes in terms and definitions e.g. new_n_n_definition/updates on definition, synonyms, references or comments. Please_n_n_mention the original term if you are suggesting correction(s).</li>_n_n_</ul>_n_n_<a name=suggested_term><b>Suggested term</b></a><font color="#666600"><font size=+1>*</font></font><b>:</b>_n_n_Type the full scientific name of the term (single name)._n_n_<p><a name=synonym><b>Synonym:</b></a> provide the synonyms if there are any. Separate the_n_n_multiple synonym terms by semi-colon (;).<b></b>_n_n_<p><a name=associated_ontology><b>Associated Ontology</b></a><font color="#666600"><font size=+1>*</font></font><b>:</b>_n_n_select the Ontology type to which the suggested new term should belong_n_n_to._n_n_<ul>_n_n_<li>_n_n_TO: Trait Ontology for plants (<a target="external" href="/documentation/../perl/ontology/search_term?id=TO:0000387"><b>Browse</b><u>)</u></a></li>_n_n__n_n_<li>_n_n_PO: Plant Ontology for plant related Morphological/anatomical terms (Under_n_n_development)</li>_n_n__n_n_<li>_n_n_GO: Gene Ontology terms for molecular function of a gene product (<a target="external" href="/documentation/../perl/ontology/search_term?id=GO:0003674"><b>Browse</a></b>)</li>_n_n__n_n_<li>_n_n_GO: Gene Ontology terms for biological process (<a target="external" href="/documentation/../perl/ontology/search_term?id=GO:0008150"><b>Browse</a></b>)</li>_n_n__n_n_<li>_n_n_GO: Gene Ontology terms for cellular component (<a target="external" href="/documentation/../perl/ontology/search_term?id=GO:0005575"><b>Browse</a></b>)</li>_n_n_</ul>_n_n_<a name=taxonomic_class><b>Taxonomic class:</b></a> If the suggested term is specific to a plant then_n_n_carefully select for dicot or monocot and if others is the option, please_n_n_specify._n_n_<p><a name=definition><b>Definition of the suggested term</b></a><font color="#666600"><font size=+1>*</font></font><b>:</b>_n_n_try to provide the precise scientific definition for the suggested term._n_n_The field should be used for New term/New suggestion for a relationship/correction_n_n_(from the field "Submission type")._n_n_<p><a name=parent_terms><b>Parent terms:</b></a>_n_n_<br>&nbsp;_n_n_<ul>_n_n_<li>_n_n_<b>Parent term 1:</b> mention the parent term if any available from the_n_n_presently available ontology terms.</li>_n_n__n_n_<ul>_n_n_<li>_n_n_<b>Relationship to parent:</b> select if the suggested term should be considered_n_n_as a <u>part of</u> (is a parent of ) or <u>is an instance of</u> (child_n_n_of) the parent term.</li>_n_n__n_n_<li>_n_n_<b>Parent ontology ID No:</b> mention the TO/PO/GO ID of the parent term,_n_n_if known.</li>_n_n_</ul>_n_n__n_n_<li>_n_n_<b>Parent term 2:</b> same as for Parent term 1. Important thing to observe_n_n_here is that the DAG allows terms to have multiple parent-child relationships_n_n_unless a cycle is created, which is not allowed.</li>_n_n__n_n_<ul>&nbsp;_n_n_	0
protein	Protein Search	_n_n_<blockquote>_n_n_<center>_n_n_<font face="Arial,Helvetica"><font size=+1><b>Rice Protein Database Search</b>&nbsp;&nbsp;[<a target="external" href="/perl/protein_search">&nbsp;SEARCH PROTEIN&nbsp;</a>]</font></font></center>_n_n_<br>_n_n_<li>_n_n_<font face="Arial,Helvetica"><b>Search: </b><font size=-1>You can search _n_n_rice protein database using either of the SWISSPROT accesion number / SPTrEMBL ID / protein name / gene name / subspecies / cultivar. <br><br>If your query finds more than 500 matching records, only the first 500 records will be displayed._n_n_ To see all the matching records you will be directed to an another link, showing only the Accession numbers in a table. _n_n_This table will not give you an extended view of Protein name, Organism (subspecies-cultivar) and Evidence codes. However,the_n_n_accession numbers will carry a hotlink to the entry in our rice protein database._n_n_</font></font></li>_n_n__n_n_</blockquote>_n_n_<blockquote>_n_n_<center>_n_n_<font face="Arial,Helvetica"><font size=+1><b>Rice Protein page</b></font></font></center>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><b>General Information:</b> </font></li>_n_n_</blockquote>_n_n__n_n_<ul>_n_n_<ul>_n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Name(s):&nbsp; </b>Shows_n_n_all the different names by which the molecule is represented in various_n_n_databases and in scientific literature.</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>E.C. Number(s):&nbsp; </b>Shows_n_n_the designated <a target="external" href="http://www.chem.qmw.ac.uk/iubmb/enzyme/">Enzyme_n_n_Commission</a> (E.C.) number. The EC numbers link to the <a target="external" href="http://www.genome.ad.jp/dbget-bin/www_bfind?enzyme">GenomeNet</a>,_n_n_Japan</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Gene name(s):&nbsp; </b>Lists_n_n_all the gene names by which the molecule is called, as designated by the_n_n_<a target="external" href="http://mbclserver.rutgers.edu/CPGN/index.html">Commission_n_n_on Plant Gene Nonmenclature</a>.</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Genome Browser:</b> It links the protein entry to the respective protein sequence on the <a target="external" href="/perl/helpview?se=1&kw=contigview">Rice Genome Browser.</a></font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Accession number:&nbsp; </b>Is_n_n_the <a target="external" href="http://www.expasy.org/sprot/">Swissprot </a>accession number,_n_n_also similar to the "AC" field from <a target="external" href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1uEaX1He_oL+-lib+SWALL">SWALL</a>_n_n_(EMBL) record and "ACCESSION" field of the <a target="external" href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Protein">GenBank</a>_n_n_records of the respective protein entry. Links the protein entry to the_n_n_other databases namely, <a target="external" href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Protein">GenBank_n_n_protein database</a>,&nbsp; <a target="external" href="http://srs6.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1uEaX1He_oL+-lib+SWALL">SWALL</a>_n_n_from EMBL and <a target="external" href="http://www.expasy.org/sprot/">SWISS-PROT</a>.</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Organism:</b>&nbsp; Represents_n_n_the taxonomy of the organism from which the protein sequence was derived.</font></font></li>_n_n__n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>&nbsp;Species:</b>&nbsp;_n_n_Shows the <a target="external" href="http://www.ncbi.nlm.nih.gov:80/htbin-post/Taxonomy/wgetorg?mode=Undef&id=4527&lvl=3&keep=1&srchmode=1&unlock">species</a>_n_n_of the Genus <i><a target="external" href="http://www.ncbi.nlm.nih.gov:80/htbin-post/Taxonomy/wgetorg?mode=Info&id=4527&lvl=3&keep=1&srchmode=1&unlock">Oryza</a></i></font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1>&nbsp;<b>Subspecies:&nbsp;</b>_n_n_The subspecies <a target="external" href="http://www.ncbi.nlm.nih.gov:80/htbin-post/Taxonomy/wgetorg?mode=Info&id=39946&lvl=3&keep=1&srchmode=1&unlock">Indica_n_n_</a>or_n_n_	0
blast	Blast Search	_n_n_<!-- <ul>_n_n_  <li> -->_n_n_    <dl>_n_n_      <dt><b>General information</b></dt>_n_n_      <dd><br>BLAST stands for <b><u>B</u></b>asic<b>_n_n_<u>L</u></b>ocal <b><u>A</u></b>lignment <b><u>S</u></b>earch <b><u>T</u></b>ool_n_n_and was developed by <a target="external" href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=91039304&form=6&db=m&Dopt=r">Altschul_n_n_et al. (1990)</a> and significantly improved by <a target="external" href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r">Altschul_n_n_et al. (1997)</a>. It is a very fast search algorithm that is used separately_n_n_for protein or DNA databases. and is best used for sequence searching,_n_n_rather than for motif searching. Gramene provides BLAST facility for the_n_n_Grasses. To search other datasets&nbsp; and access further information_n_n_on BLAST resources, help document and BLAST 2.0 Release,&nbsp; please refer_n_n_to <a target="external" href="http://www.ncbi.nlm.nih.gov:80/BLAST/">http://www.ncbi.nlm.nih.gov:80/BLAST/</a>.<p></p></dd>_n_n_    </dl>  _n_n_<!--  </li>_n_n_  <li> -->_n_n_    <dl>_n_n_      <dt><b>BLAST methods</b></dt>_n_n_      <dd> _n_n_        <p>The NCBI BLAST family of programs includes:</p>_n_n_        <ul>_n_n_          <li>blastp: Compares an amino acid query sequence against a protein sequence database.</li>_n_n_          <li>blastn: Compares a nucleotide query sequence against a nucleotide sequence Database.</li>_n_n_          <li>blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.</li>_n_n_          <li>tblastn: Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.</li>_n_n_          <li>tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.</li>_n_n_        </ul>_n_n_      <p></p>_n_n_      </dd>_n_n_    </dl>  _n_n_<!--  </li>_n_n_  <li> -->_n_n_    <dl>_n_n_      <dt><b>Databases</b></dt>_n_n_      <dd> _n_n_        <br>_n_n_        <ul>_n_n_          <li>Rice Protein sequences from SwissProt/TrEMBL. This data are kindly provided by their ftp site.</li>_n_n_          <li>TIGR Rice Gene Index representing a clustering analysis of the public ally available rice ESTs. This data are kindly provided by TIGR FTP site.</li>_n_n_          <li>Genbank Rice BAC/PAC Sequences All Rice Genomic clones sequenced by the International rice-sequencing project (IRSP).</li>_n_n_          <li>Genbank Rice BAC ends</li>_n_n_          <li>Genbank Rice ESTs</li>_n_n_          <li>Genbank Barley ESTs</li>_n_n_          <li>Genbank Maize ESTs</li>_n_n_          <li>Genbank Wheat ESTs</li>_n_n_        </ul>_n_n_      <p></p>_n_n_      </dd>_n_n_    </dl>  _n_n_<!--  </li>_n_n_  <li> -->_n_n_    <dl>_n_n_      <dt><b>Running Blast</b></dt>_n_n_      <dd><br>To run Blast, a query sequence must be supplied by directly pasting the sequence in the text box.  The examples of the sequence format are provided below. Select the appropriate blast program and dataset_n_n_you want to query. Blast will run immediately and provide a summary table_n_n_of results.<p></p>_n_n__t_t_<p>Examples:_n_n_        <p>_n_n_        <ul>_n_n_          <li>FASTA format_n_n_            <p><b>>gi|11026061|gb|AU162662.1|AU162662 AU162662 Rice mature leaf Oryza sativa cDNA clone S20357, mRNA sequence_n_n_CTCTCTTGGTTTCTCTCTCTAGCCATCGGCTGCCTCTCTCTCTCTCTCTCTCCTCGCTGCCCCATAGGTG_n_n_GACGCGGGTCAACGGGCCGGTCGCCGGCGGGGCGGCTGCGGCGGCGAGAGGAGGTAGAAGCTCCGGCGAT_n_n_CGCGAGGGCAGGCGGCGGGTTGGTGCGCTGCCGGCTTCGAGTTCGAGCGGGCGGGCCATGGGGAGGAACG_n_n_GGAGCGTCAAGCGTACGTCGTCGTCGGGGGCGGCGGCGGCGTTCACGGCGAATCCCCGCGACTACCAGCT_n_n_CATGGAGGAGGTCGGGTACGGGGCGCACGCCGTTCGTGTACCGCGCGCTGTTCGTCCCCAGGAACGACGT_n_n_CGTGGCTGTCAAGTGCCTGGATCTCGATCAGCTTCAACAACAANATCGATGAAATCCAACGGGAGGCTCA_n_n_AATCATGAGCTTGATAGAGCATCCTAATGTCATCAGGGCTTACTGCTCATTTGTTTGTTGAGCACAGCCT_n_n_TTGGGGTAGTAATGCCATTTTATGACTGAGGGTTCATGTCTTGCACCTAATGAAGATTGCATATCCTGAT_n_n_TGGTTTTCGAGGAAACTTGTTAATTTGGGCTCTAATTCTAAAGGAAAACACTTTAANGGCTTTTGGAAGT_n_n_ACCTTCAAAAGGCAAGGACAAATCCATCGTGATGTCAAAGGCCGGCAATATCCCTTGTTGATAATGCTGG_n_n_TATAGTGNAACT</b></p>_n_n_          </li>_n_n_        <li>Raw text format_n_n_	0
blast	Blast Search	            <p><b>CGCGAGGGCAGGCGGCGGGTTGGTGCGCTGCCGGCTTCGAGTTCGAGCGGGCGGGCCATGGGGAGGAACG_n_n_GGAGCGTCAAGCGTACGTCGTCGTCGGGGGCGGCGGCGGCGTTCACGGCGAATCCCCGCGACTACCAGCT_n_n_CATGGAGGAGGTCGGGTACGGGGCGCACGCCGTTCGTGTACCGCGCGCTGTTCGTCCCCAGGAACGACGT_n_n_CGTGGCTGTCAAGTGCCTGGATCTCGATCAGCTTCAACAACAANATCGATGAAATCCAACGGGAGGCTCA_n_n_AATCATGAGCTTGATAGAGCATCCTAATGTCATCAGGGCTTACTGCTCATTTGTTTGTTGAGCACAGCCT</b></p>_n_n_          </li>_n_n_        </ul>_n_n_      </dd>_n_n_    </dl>  _n_n_<!--  </li>_n_n_ _n_n_  <li> -->_n_n_    <dl>_n_n_      <dt><b>Results Summary</b></dt>_n_n_      <dd><br>Your BLAST request will run_n_n_immediately and return results directly to your Web Browser in HTML format._n_n_The "Sequence" field will return the Accession numbers of the high scoring_n_n_hits. The "Description" contains the brief description available from the_n_n_FASTA format. By selecting the "Details" section it will take you directly_n_n_to the BLAST alignment of the query sequence with the respective accession_n_n_(sbjct) from the query database.<p></p></dd>_n_n_    </dl>  _n_n_<!--  </li>_n_n_ _n_n_</ul> -->_n_n_	1
ensembl	EnsEMBL	To make the  sequence/feature/gene database and the contig viewer, gene viewer_n_n_and these help pages,_n_n_we started with version 1.00 of <a href="www.ensembl.org" target="external">EnsEMBL</a>, adapted it to using Oracle and_n_n_having a non-assembled genome, and added additional tracks, marker information, etc._n_n_Thanks to Ewan Birney, James Stalker, Michelle Clamp, Arne Stabenau, and Nicole Redaschi of the EnsEMBL team_n_n_for helpful discussions._n_n_	0
seqentryview	Clone/Contig viewer	<p>"SeqentryView" allows you to view and dump the contigs that make up a clone.</p>_n_n__n_n_<p>The top of the page gives the Clone identifier(Genbank Accession),_n_n_along with the Contig identifier. Below that is the Clone name and _n_n_sequencing status. </p>_n_n__n_n_<p>Below the page header is a table showing a graphical display for this Contig._n_n_The image is similar to those in "ContigView" (see <a href="HELP_contigview_HELP">help on "ContigView"</a>),_n_n_in that you can click on the features displayed to get more information._n_n_It does not display ESTs.</p>_n_n__n_n_<p>If you wish to see all contigs in a clone, click on the "View all #_n_n_contigs" link at the top of the page. Alternatively, click on "contig_n_n_map" to get the "ContigView" page for this region</p>_n_n__n_n_<p>Under each contig image is a "Dump this region" link. Clicking on_n_n_this will take you to a page where you can configure the_n_n_<a href="HELP_dumpcfgview_HELP">flatfile dumping</a> of that contig. A_n_n_similar link below enables you to dump the entire clone.</p>_n_n__n_n_<p>The search box at the top of this page allows you to search for any identifier present in the sequence database (see <a href="HELP_search_HELP">Sequence Database Search</a>).</p>_n_n_	0
helpview	Context-Sensitive Help	<p>_n_n_Clicking on the <img src="/gfx/helpview/help.gif" align="absmiddle" alt="Help"> icon will pop up a window containing context-sensitive help on the subject. You may also search the help database using the box provided in the top of this window. Click on "index" to see a list of all available "Help" and "How Do I..." pages  </p>_n_n_<p>_n_n_<a href="HELP_howto_HELP">How do I...?</a> pages are provided as part of Gramene Help.  These pages guide you through some typical usages of Gramene._n_n_</p>_n_n__n_n_These help pages were made by editing and adding to those supplied with <a href="HELP_ensembl_HELP">EnsEMBL</a>._n_n_	0
browser	Navigation bar Search / "Class Browser" / "Search the Gramene Database"	<p>Search the Acedb database which Gramene inherited from RiceGenes._n_n_Also, <a href="/newsletters/rice_genetics/">Rice Genetics Newsletters</a> and Rice Genomic Newsletters._n_n_'*' is a wildcard matching any sequence of characters._n_n_If you use the navigation bar box or choose 'Anything' it will also search the <a href="HELP_search_HELP">sequence database</a>, <a href="HELP_protein_HELP">proteins</a>, and <a href="HELP_vocabulary_HELP">ontology terms</a>._n_n_</p>_n_n_<p>_n_n_To do an unrestricted text search on the Acedb database , check the_n_n_Detailed search (long) box and choose "Anything"._n_n_For a more structured search, use _n_n_<a href="/gramene/searches/query" target="external">Acedb Query</a>_n_n_</p>_n_n_<p>Help on the contents of Gramene's Acedb database is available_n_n_<a href="http://www.gramene.org/gramene/searches/query?query=find%20HELP" target="external">here</a>.</p>_n_n_	0
search	Sequence Database Search	<p>The search box at the top of each Gramene Ensembl page allows you to_n_n_search the whole sequence database ("Find 'All' ") or restrict the_n_n_search to a specific identifier present in the sequence database.  Use_n_n_"Find 'Object in acedb'" to search the <a href="HELP_browser_HELP">Acedb database</a> _n_n_instead of the Sequence Database._n_n_</p>_n_n_<p align="center">_n_n_<img src="IMG_unisearch_box.png_IMG" alt="search box"></p>_n_n__n_n_<h4>Restricted Search</h4>_n_n_<p>Select the type of identifier you are looking for from the drop-down_n_n_list to the left of the search box (Gene, Contig, Clone, BAC end,_n_n_Protein, Map marker) and type the identifier into the search box._n_n_Use "*" as a wildcard._n_n_"Protein" searches the Protein database, not the Sequence database._n_n_Use <a href="HELP_protein_HELP">protein_search</a> to search the_n_n_Protein database in depth.<br>_n_n_Click the <img src="/gfx/lookup.gif" align="absmiddle" alt="search">_n_n_<br>There are context-type-sensitive examples shown to the right end of the box._n_n_</p>_n_n__n_n_<h4>Find 'All'</h4>_n_n_<p>If you aren't sure about the type of identifier you are trying to find, select 'All' in the drop-down box, and all indices are searched.  Acedb objects are not included in 'All', but Proteins are.<br>_n_n_</p>_n_n__n_n_<h4>Search Results Page</h4>_n_n_<p>_n_n_If you searched for a specific type of identifier by selecting it from_n_n_the search drop-down box, e.g. "Gene", then you will see a page of_n_n_results for that type._n_n_</p>_n_n_<p>_n_n_Each search result is a link to a page giving more detail._n_n_If there is only one hit you will be taken directly to this entry._n_n_For BAC ends, the link goes to a <a href="HELP_contigview_HELP">contigview</a> _n_n_page which displays the BAC end hit to the genome in context.  You can_n_n_go to the Genbank record for the BAC end from there._n_n_</p>                       _n_n_	0
contigview	Sequence Contig Displays	<p>"ContigView" is the principal tool for visualizing the sequence database.  It provides a high level view of clones, genes and other features that have been placed on them.</p>_n_n__n_n_<p>_n_n_The top half of the display shows an overview of the clone (by default 200Kb of DNA is shown). The red box is represented in the detailed view below it. <br>_n_n_The absolute base pair location on the clone of the red box is indicated in the navigator bar at the bottom of the page. You can use this bar to navigate along any clone by entering a new chromosome_clone and/or basepair location._n_n_</p>_n_n__n_n_<h3>Overview</h3>_n_n__n_n_<p align="center">_n_n_<img src="/gfx/buttons/changefeatures.png" alt="comment"></p>_n_n_<p>_n_n_This button above the overview allows you to configure the look of the "Overview" (see <a href="HELP_config_HELP">Configuration</a> for more details)._n_n_</p>_n_n_<p>_n_n_The individual contigs are shown in alternating dark and light blue.  A horizontal line indicates a gap in the sequence assembly.</p>_n_n__n_n_<p align="center">_n_n_<img src="IMG_contigviewtop.png_IMG" alt="comment">_n_n_</p>_n_n__n_n_<p>_n_n_Markers are indicated in magenta and cyan (for ssr's) under the contig map.  Red boxes represent genes. _n_n_BAC ends are green. _n_n_Rice ESTs from dbEST are represented in red: each exon is a box joined by lines above and below._n_n_ Other ESTs are shown similarly in shades of yellow and orange._n_n_At present, the only genes shown are those that were annotated by the clone's submitter._n_n_If the gene is in SPTREMBL, its name there will be shown, otherwise an arbitray sequential name (Gene1, Gene2, ... )_n_n_Above the contig map a small scale bar is given.  </p>_n_n_<p>_n_n_You may click anywhere on this view to recenter the red box at that point on the contig map.  The lower display will change accordingly</p>_n_n__n_n_<h3>Navigator Buttons</h3>_n_n_<p align="center">_n_n_<img src="/gfx/buttons/dump.gif" alt="comment"></p>_n_n_<p>_n_n_This dump button allows you to dump the specified region as a flat file (see <a href="HELP_dumpcfgview_HELP">Flatfile Dumping</a>)._n_n_</p>_n_n__n_n__n_n_<p align="center">_n_n_<img src="/gfx/buttons/win_left.gif" alt="comment">_n_n_<img src="/gfx/buttons/win_right.gif" alt="comment">_n_n_</p>_n_n_<p>Clicking on one of these two buttons will scroll the whole display to the left or right by 80% of the current display length. The size of the red box will not change.</p>_n_n__n_n_<p align="center">_n_n_<img src="IMG_zoom.gif_IMG" alt="comment">_n_n_</p>_n_n_<p>By default the red box represents 50kb. These buttons give you the option to zoom in and out, varying the size of the DNA fragment in the red box from 50 bases up to 1 Mb.  Use this to restrict or expand the field of view to a scale suitable to view any feature of interest.</p>_n_n__n_n_<p align="center">_n_n_<img src="/gfx/buttons/changefeatures.png" alt="comment"></p>_n_n_<p>_n_n_This button allows you to configure the look of the "Detailed View" (see <a href="HELP_config_HELP">Configuration</a> for more details)._n_n_</p>_n_n__n_n_<h3>Detailed View</h3>_n_n_<p>_n_n_The lower red box ("Detailed View") shows the sequence features in more detail and information concerning sequence annotations is provided. The DNA sequence is again represented as alternating dark and light blue contigs.  The colour-coded features above the contigs are positioned on the forward strand, those below on the reverse strand.  _n_n__n_n_Mouseover and "tooltip" text will show the feature's name and a link to more detailed information where available.</p>_n_n_<p align="center">_n_n_<img src="IMG_contigviewbottom.jpg_IMG" alt="comment"></p>_n_n__n_n_<p>_n_n_<b>DNA (contigs)</b><br>_n_n_Hovering the mouse cursor over the contig bar will give you the option to see more information about the contigs in "<a href="HELP_seqentryview_HELP">SeqentryView</a>"._n_n__n_n_<p>_n_n_<b>Transcripts</b><br>_n_n_"Detailed View" does not display genes as such but rather their_n_n_transcripts.  Ensembl considers genes as a collection of exons - from_n_n_which there may be many transcripts.  At present the only transcripts_n_n_in our database are those annotated by the sequencing centers, and are_n_n_red as if they were_n_n_	0
contigview	Sequence Contig Displays	"known transcripts" generated by Ensembl._n_n_"External transcripts" would be either green (curated as gene) or gray_n_n_(curated as pseudogene), _n_n_Ensembl "novel transcripts" would be black.  If there are_n_n_several transcripts at the same point on the sequence then that gene_n_n_has been assessed as producing multiple transcripts (displayed on_n_n_different lines).  _n_n_Mouseover on a transcript_n_n_</p>_n_n_<p align="center">_n_n_<img src="IMG_contigviewprotein.jpg_IMG" alt="comment"></p>_n_n__n_n_<p>_n_n_will produce a menu with the name of the transcript _n_n_(the SwissProt id of any corresponding protein,_n_n_otherwise the _n_n_<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein" target="external">_n_n_Genbank Protein_n_n_Database</a> id, or a Gramene id)_n_n_at the top:<br>_n_n__n_n_<ul>_n_n_<li><b>Transcript information</b> will take you to "<a href="HELP_geneview_HELP">GeneView</a>", providing data on the predicted gene</li>_n_n__n_n_<li><b>Protein information</b> will take you to "<a href="HELP_protein_HELP">the Gramene protein page</a>" if there is SwissProt or curated information on the protein or to  "<a href="HELP_protview_HELP">EnsEMBL ProteinView</a>", providing data on the predicted protein</li>_n_n__n_n_<li><b>Protein sequence (FASTA)</b> will take you to "DumpView", showing the peptide sequence in FASTA format.</li>_n_n__n_n__n_n_<li><b>cDNA sequence</b> will take you to "DumpView", showing the CDNA sequence for this transcript in FASTA format.</li>_n_n_</ul>_n_n_</p>_n_n__n_n_<p>_n_n_The following features are strand independent and are shown at the bottom of the "Detailed View"._n_n_</p>_n_n__n_n_<p>_n_n_<BAC Ends>_n_n_These are <a href="/documentation/bac_bacend_documentation.txt" target="external">CUGI Bacends</a>._n_n_Mouseover and "tooltip" text will show the id of this marker and the_n_n_option to view the sequence of the BAC end in Genbank._n_n_</p>_n_n__n_n_<p>_n_n_<b>Markers on Rice Maps</b><br>_n_n_These are <a href="/documentation/bac_marker_documentation.txt" target="external">JRGP/Cornell Markers</a>._n_n_Mouseover and "tooltip" text will show the id of this marker and the_n_n_option to view the details in <a href="HELP_markerview_HELP">"MarkerView"</a> _n_n_or the sequence of the marker in Genbank._n_n_</p>_n_n__n_n_<p>_n_n_<b>Rice SSR Marker</b><br>_n_n_These are <a href="/documentation/bac_ssr.txt" target="external">Cornell Rice SSRs</a>._n_n_Mouseover and "tooltip" text will show the id of this marker and the option to view the details in <a href="HELP_markerview_HELP">"MarkerView"</a>._n_n_</p>_n_n__n_n_<p>_n_n_<b>Rice CDS</b>_n_n_These are <a href="/documentation/EST/oryza_cds.txt" target="external">Complete Coding Sequences from Genbank</a>_n_n_Mouseover and "tooltip" text will show the Genbank id and the option to view this Genbank entry._n_n_</p>_n_n__n_n_<p>_n_n_<b>Rice TIGR Gene Index</b>_n_n_These are the results of mapping _n_n_<a href="/documentation/EST/tigr_oryza.txt" target="external">_n_n_predicted transcripts from TIGR's non-redundant view of rice genes_n_n_</a>_n_n_Mouseover and "tooltip" text will show the TIGR id and the option to view the TIGR OsGI TC Report._n_n_</p>_n_n__n_n_<p>_n_n_<b>Maize TIGR Gene Index</b>_n_n_These are the results of mapping _n_n_<a href="/documentation/EST/tigr_maize_gi.txt" target="external">_n_n_predicted transcripts from TIGR's non-redundant view of maize genes_n_n_</a>_n_n_Mouseover and "tooltip" text will show the TIGR id and the option to view the TIGR ZmGI TC Report._n_n_</p>_n_n__n_n_<p>_n_n_<b>ESTs</b><br>_n_n_These tracks show <a href="/documentation/index.html#est" target="external">alignments to the rice genome</a> of rice and other grain mRNA_n_n_transcripts deposited in the <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Nucleotide" target="external">Genbank Nucleotide Sequence Database</a>.  _n_n_Mouseover and "tooltip" text will show the Genbank id and the option to view this Genbank entry._n_n_</p>_n_n__n_n_<p>_n_n_<b>Repeats</b><br>_n_n_This indicates a region of repetitive sequence._n_n_</p>_n_n__n_n_<p>_n_n_<b>%GC</b><br>_n_n_The plot shows you the relative GC content._n_n_</p>_n_n__n_n_<h3>Navigator Bar</h3>_n_n_<p>_n_n_	1
contigview	Sequence Contig Displays	The Navigator bar allows you to navigate along any clone by giving a location. It also gives you the option to turn off the menus and image maps (after click on <img src="/gfx/buttons/refresh.gif" align="absmiddle" alt="Help">) which can improve browsing speed at the expense of display functionality._n_n_</p>_n_n__n_n_<p>_n_n_The search box at the top of the page allows you to search for any identifier present in the sequence database (see <a href="HELP_search_HELP">Sequence Database Search</a>).</p>_n_n__n_n_</p>_n_n_	2
protview	Ensembl Protein Report	<p>"ProteinView" provides information about a particular protein in the _n_n_sequence database.  Proteins in SwissProt and curated proteins have a _n_n_<a href="HELP_protein_HELP">more detailed page</a> available.  </p>_n_n__n_n_<p>The summary table at the top of the report provides the following data about the protein:_n_n_<ul>_n_n__t_t_<li><b>Gramene Protein ID</b> - the Gramene protein identifier.</li>_n_n__t_t_<li><b>Gramene Gene</b> - the corresponding Gramene gene identifier.</li>_n_n__t_t_<li><b>Description</b> - the name of the protein.</li>_n_n__t_t_<li><b>Prediction Method</b> - how the protein was predicted.</li>_n_n__t_t_<li><b>Protein structure</b> - a map showing protein domains (e.g. Pfam) and  protein features (transmembrane, low complexity and coli regions).</li>_n_n_</ul>_n_n_<p>Below the summary table are a series of detailed tables describing the protein</p>_n_n_<ul>_n_n__t_t_<li><b>Peptide sequence</b> - the sequence in Fasta format, together with the peptide properties and a link to transcript info in "<a href="HELP_geneview_HELP">GeneView</a>".</li>_n_n_</ul>_n_n__n_n_<p>_n_n_The search box at the top of the page allows you to search for any identifier present in the sequence database (see <a href="HELP_search_HELP">Sequence Database Search</a>).</p>_n_n__n_n__n_n_	0
markerview	Map Marker Information	<p>"MarkerView" displays information about a particular map marker.</p>_n_n_<p>First, a link to the page for this _n_n_<a href="/gramene/generic/tree?name=CLICK_HERE_FOR_Marker_Info&class=LongText" target="external">marker in the acedb database</a> is given._n_n_If the marker has a sequency entry in Genbank, a link to that is given also.</p>_n_n_<p>The table on this page shows information about the sequenced_n_n_clone(s) to which the marker is mapped, including the position in the_n_n_clone and links to view or download the clone.  This table is omitted if_n_n_this marker is not currently mapped to any sequenced clone(s)._n_n_</p>_n_n__n_n__n_n__n_n__n_n_<p>The search box at the top of the page allows you to search for any identifier present in the sequence database (see <a href="HELP_search_HELP">Sequence Database Search</a>).</p>_n_n_	0
maps	Genetic & Comparative Maps	_n_n_<p>_n_n_The genetic and comparative maps allow one to view graphical_n_n_representations of genetic maps and compare them to other genetic and_n_n_physical maps from other species and studies.  <em>Please note:</em>  _n_n_Enabling Javascript will cause forms to be submitted automatically_n_n_after choosing from the drop-down lists.  This is intended to be a_n_n_convenience for the user but is not a requirment for using the maps._n_n_</p>_n_n__n_n_<p>_n_n_<b>Reference Map Study</b>_n_n_<br>_n_n_Choose a reference map study. The studies are sorted alphabetically_n_n_by species and study names.  For a list of all the map studies, _n_n_see the <a target="external" href="/maps/map_studies">Map Study Info</a> page._n_n_</p>_n_n__n_n_<p>_n_n_<b>Reference Map</b>_n_n_<br>_n_n_A list of possible reference linkage groups (also referred to here_n_n_as &quot;maps&quot;) in the chosen map study will be presented next,_n_n_named and ordered by linkage groups. Select one._n_n_</p>_n_n__n_n_<p>_n_n_<b>Comparative Map</b>_n_n_<br>_n_n_Once you have chosen the reference linkage group and the map has been_n_n_displayed, you will also be presented with the following form elements:_n_n_<ul>_n_n_  <li>_n_n_    The <b>start</b> and <b>end</b> positions of the reference linkage_n_n_    group <em>(optional)</em>. If omitted, the entire map will be_n_n_    shown. The positions can be given in centimorgan positions or loci_n_n_    names. If a marker cannot be found for the start or stop, then it_n_n_    will be ignored._n_n_  </li>_n_n_  <li>_n_n_    An input for map elements (map features or contigs) to_n_n_    <b>highlight</b> <em>(optional)</em>. Separate multiple elements_n_n_    with commas, spaces, colons, semi-colons or whitespace._n_n_  </li>_n_n_  <li>_n_n_    The <b>comparative maps</b> available. Only the genetic and physical_n_n_    maps which have some relationships to the reference linkage group_n_n_    will be shown. The maps are sorted by their species and map study_n_n_    names. Choose either a single map or an entire map study to view and_n_n_    then press the &quot;Submit&quot; button._n_n_  </li>_n_n_  <li>_n_n_    The ability to <b>show or hide discordant contigs</b>. This option_n_n_    is only applicable when a physical map is being displayed and is_n_n_    always <em>optional</em>. The default is to display all contigs._n_n_  </li>_n_n_</ul>_n_n_</p>_n_n__n_n_<p>_n_n_<b>Navigating the Maps</b>_n_n_<br>_n_n_To view different regions of the reference linkage group in greater_n_n_detail, simply click on the area which interests you.  Continue_n_n_clicking until you are at the maximum magnification (when an area no_n_n_less than 2 centimorgans will be displayed).  Click the &quot;Up&quot;_n_n_or &quot;Down&quot; buttons at the top of the map to move up or down,_n_n_respectively.  These buttons will be disabled if the entire linkage_n_n_group is already being displayed.  You can also move up or down by_n_n_clicking on the extreme ends of the map if the ends have small arrows_n_n_indicating that the map extends further._n_n_</p>_n_n__n_n_<p>_n_n_You can also enlarge and reduce the areas shown in the map by clicking_n_n_on the &quot;Zoom In&quot; or &quot;Zoom Out.&quot;  Clicking on_n_n_&quot;Zoom In&quot; will show an smaller area centered on the current_n_n_area.  Note that the map will always attempt to show some map_n_n_features, so the region selected may be enlarged until some are shown._n_n_To return to a view of the entire map, click on &quot;Full View&quot;_n_n_at any time._n_n_</p>_n_n__n_n_<p>_n_n_When a entire map study is chosen as the comparative map, you can view the_n_n_reference linkage group alongside any one of the individual maps (genetic_n_n_linkage groups or physical contigs) by clicking on the the desired map._n_n_The resulting page will vary depending on whether the comparative map is a_n_n_genetic or physical map, but the general effect is that more information on the_n_n_specific relationships between the two maps will be shown.  If the comparative_n_n_map is a genetic map, then clicking on the map in the detailed view will allow_n_n_the user to make that linkage group the reference map of a new view._n_n_</p>_n_n__n_n_<p>_n_n_<a name="physical_maps"></a>_n_n_<b>Viewing Physical Maps</b>_n_n_<br>_n_n_When viewing a genetic map with a physical map, the discordant contigs (those_n_n_	0
maps	Genetic & Comparative Maps	with a majority of discordant features in relation to the current reference_n_n_map) will be displayed in a red outline.  Additionally, these discordant_n_n_contigs will be pushed further to the right of the concordant contigs.  _n_n_</p>_n_n__n_n_<p>_n_n_When viewing a single contig in relation to the reference map, the_n_n_individual features which are discordant will also be shown in red._n_n_The detailed view of a contig will also include a table describing_n_n_each feature in greater detail.  Each feature name is a hyperlink to_n_n_an appropriate database to learn more about the feature.  Discordant_n_n_features in the table will be shown in grey.  Transposed features will_n_n_be highlighted in the table in yellow.  Each feature on the physical_n_n_map will also include all the other loci of genetic maps on which they_n_n_occur.  If the map study in the table is hyperlinked, then you_n_n_can click on the map study name to show the contig in relation to that_n_n_map study and linkage group._n_n_</p>_n_n__n_n_<p>_n_n_If the contig has sequenced clones, they will be shown as grey,_n_n_numbered lines.  The numbers have no particular meaning and are given_n_n_only to help you find the clones in the &quot;Clones&quot; table to_n_n_the left.  You can view the clone in the Genome Browser by clicking on_n_n_the clone on the map or the clone name in the table.  Also shown in_n_n_the table will be the <b>start</b> and <b>stop</b> bands for the_n_n_clone._n_n_</p>_n_n__n_n_<p>_n_n_<b>Viewing Markers</b>_n_n_<br>_n_n_More information on markers can be obtained by clicking on the_n_n_marker's name.  The result will vary depending on the species of the_n_n_marker's anchoring map:  markers from oat, wheat, and barley will be_n_n_directed to <a target="external" href="http://wheat.pw.usda.gov/index.shtml">GrainGenes</a>;_n_n_Rice markers will go to the Gramene site; maize markers will go to <a_n_n_target="external" href="http://www.agron.missouri.edu/">MaizeDB</a>; sorghum markers_n_n_will go to <a target="external" href="http://sorghumgenome.tamu.edu/">the sorghum_n_n_database</a>._n_n_</p>_n_n__n_n_<a name="marker_search"></a>_n_n_<p>_n_n_<b>Marker Search</b>_n_n_<br>_n_n_To find a specific marker, use the <a target="external" href="/maps/marker_search">Marker_n_n_Search</a> page.  Simply type in the names of the markers you wish to_n_n_find separating them by commas, colons, semi-colons or whitespace._n_n_For each one found, all the maps on which they occur will be_n_n_displayed.  Clicking on "View" will take you to the map viewer with_n_n_the appropriate marker highlighted._n_n_</p>_n_n__n_n_	1
dumpcfgview	Flatfile Dumping	<p>From "ContigView" etc, clicking on the button "view text" brings you to flatfile dumping</p>_n_n__n_n_<img src="/gfx/buttons/dump.gif" alt="Flatfile dumping button">_n_n__n_n_<p>This page allows you to configure what you would like to dump from the Gramene sequence database, and how you would like it dumped.</p>_n_n__n_n_<p>This allows you to select a specific feature to dump as a flat-file. In this context, "feature" includes genes, contigs, clones, cDNA, and transcript peptides.</p>_n_n__n_n_<p>You specify the type of feature, the feature id, and the type of_n_n_output you require. For DNA-type features you can also specify a number_n_n_of "context" basepairs to show either side of the chosen feature.  The_n_n_type of feature must fit the feature id, except that for gene, cDNA, and_n_n_peptide you may put in a gene, transcript, or translation identifier_n_n_and the corresponding object(s) of the specified type will be dumped._n_n_For clones, the id is the genbank accession, not the name._n_n_</p>_n_n__n_n_<img src="IMG_dumpcfgview_feature_annot.gif_IMG" alt="comment">_n_n__n_n_<p>The specified region is generated dynamically from the sequence_n_n_database, and then sent to your browser in the format you chose.  <em>Note_n_n_that the 'Dump a Region' tab is not currently active because the rice_n_n_genome is not assembled.</em></p>_n_n__n_n_<p>This page does <em>not</em> dump EST or BACend sequences.  They are not _n_n_in the Gramene database.  Use the_n_n_link from the tooltip menu in the_n_n_<a href="HELP_contigview_HELP">ContigView Detail Section</a> _n_n_to go to an authoritative source._n_n__n_n_	0
blastp	How do I find proteins similar to my protein sequence?	<OL>_n_n__n_n_<LI>Follow the "Blast Search" link on the Gramene navigation bar or just follow the link below.</LI>_n_n__n_n_<LI><A HREF='/gramene/searches/blast' target="external" class="grey2">Run similarity search on the Gramene BLAST Server</A>. _n_n_just paste in your sequence and choose the appropriate options. Choose _n_n_'Rice Proteins' as the database and blastp as the program or one of the_n_n_EST databases and tblastn as the program._n_n_The 'Run BLAST' button submits your_n_n_sequence to the BLAST server. _n_n_See <a href="HELP_blast_HELP">here</a> for more information.</LI>_n_n__n_n_<LI>The blast results contain hyperlinks to take you to the sequence you hit.</LI>_n_n_</OL>_n_n_	0
missinggene	What if a gene appears to be incorrectly positioned in the genome?	At present, all genes in the Gramene database are those annotated by the _n_n_sequencing sites.  Many clones are not annotated.  Perhaps the gene is _n_n_duplicated and the place you expect it to be has not yet been sequenced_n_n_and annotated.  This will become clearer in the future--we plan to have_n_n_an automated annotation of the whole sequenced genome._n_n_	0
config	Customising 'Contigview Windows'	<p>_n_n_This table allows you to change the configuration of the "Overview" _n_n_in "<a href="HELP_contigview_HELP">ContigView</a>" &#151;_n_n_if_n_n_you clicked the upper "Change Features" button &#151; or of the "Detailed_n_n_View" _n_n_if you clicked_n_n_the lower one.  It gives you the option to turn on or off the_n_n_individual features (e.g. BAC end) and change the colours according to_n_n_your preferences (not possible for 'Transcript' and '%GC').<br>_n_n_Overlapping features (e.g. ESTs) can be separated by setting the depth to 'expanded' (default setting). _n_n_</p>_n_n_<p>Use <img src="/gfx/buttons/refresh.gif" align="absmiddle" alt="Help"> on "<a href="HELP_contigview_HELP">ContigView</a>" to see the new configuration.</p>_n_n_<p>_n_n_After saving the the changes, the new configuration will be stored as a 'Cookie' on your computer.  Ensure 'Cookies' are enabled in your browser preferences if you want to use this configuration option._n_n_<br>Use <img src="IMG_reset.gif_IMG" align="absmiddle" alt="Help"> to get the default configuration. _n_n_</p>_n_n_	0
geneview	Ensembl Gene Report	<p>"GeneView" provides detailed information about a particular Gramene gene.</p>_n_n__n_n_<p>The summary table at the top of the report provides the following data about the gene:_n_n_<ul>_n_n__t_t_<li><b>Ensembl gene ID</b> - the Gramene gene identifier.</li>_n_n__t_t_<li><b>Genome Location</b> - the chromosome containing this gene with a link to "<a href="HELP_contigview_HELP">ContigView</a>".</li>_n_n__t_t_<li><b>Description</b> - a short description of the gene.</li>_n_n__t_t_<li><b>Predicted Transcripts</b> - a list of predicted_n_n__t_t_transcripts for this gene with links to the transcript_n_n__t_t_structure below and to "<a href="HELP_protview_HELP">ProteinView</a>". _n_n__t_t_If the translation of this transcript matches a SwissProt or curated protein, there is also a link to <a href="HELP_protein_HELP">the Gramene Protein page</a> </li>_n_n__t_t_<li><b>Links</b> - Every gene has a link to Genbank, to the protein as annotated by the sequencing center.  Genes with a translation which matches a SwissProt or TREMBL protein have an additional link to SPTREMBL._n_n_</ul>_n_n_<p>A <a href="HELP_dumpcfgview_HELP">text dump</a> of the whole gene, including introns, is available here. (The transcript is available below).</p>_n_n__n_n_<p>Below the summary table are a series of detailed tables describing the gene's predicted transcripts, sequence information, exons, and splice-sites.</p>_n_n__n_n_<p>The Predicted Spliced Sequence Information table has a link to a cDNA sequence for the transcript which can be copied and pasted.</p>_n_n__n_n_<p>_n_n_The search box at the top of the page allows you to search for any identifier present in the sequence database (see <a href="HELP_search_HELP">Sequence Database Search</a>).</p>_n_n_	0
SeqTable.cgi	Rice BAC/PAC Sequence Information	<p>_n_n_This page shows all sequenced Clones on a Rice Chromosome._n_n_<ul>_n_n_<li>The clone names in the first column are links to the Gramene_n_n_<a href="HELP_contigview_HELP">"ContigView"</a> page for the clone._n_n_<li>The Sequencing Site abbreviations link to the site's home page._n_n_<li>The DNA length links to a FASTA file (at Genbank)._n_n_<li>The Accession number links to the Genbank entry for this clone._n_n_</ul>_n_n_You may click on any column heading(except Fragments) to sort the table by that column,_n_n_or reverse the sort._n_n_Sorting by HTG Phase implies the reverse sorting by number of fragments._n_n_So Sorting from highest to lowest Phase (the default) implies sorting from least to most _n_n_fragments within that (and annotated clones before unannotated)._n_n_</p>_n_n_	0
protein	Protein Search	the <a target="external" href="http://www.ncbi.nlm.nih.gov:80/htbin-post/Taxonomy/wgetorg?mode=Info&id=39947&lvl=3&keep=1&srchmode=1&unlock">Japonica</a>_n_n_of the rice species <i><a target="external" href="http://www.ncbi.nlm.nih.gov:80/htbin-post/Taxonomy/wgetorg?mode=Undef&id=4530&lvl=3&keep=1&srchmode=1&unlock">Oryza_n_n_sativa</a></i>.</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1>&nbsp;<b>Cultivar:&nbsp;</b>_n_n_Is the variety/cultivar name from which the sequence was derived.</font></font></li>_n_n_</ul>_n_n_</ul>_n_n_</ul>_n_n_</ul>_n_n__n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><b>Associations:</b></font></li>_n_n_</ul>_n_n__n_n_<ul>_n_n_<ul>_n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1>&nbsp;<b>Gene Ontology (<a target="external" href="http://www.geneontology.org">GO</a>)_n_n_mappings (GO-Interpro-Rice mapping)</b></font></font></li>_n_n__n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b><i><u>Molecular function:</u></i></b>&nbsp;_n_n_List of GO term(s) that defines the <a target="external" href="/perl/ontology/search_term?id=GO:0003674">molecular_n_n_function</a> of the protein molecule (protein entry)</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><i><u><b>Biological process</b></u></i>:</font></font><font face="Arial,Helvetica"><font size=-1>&nbsp;_n_n_List of GO term(s) defines the <a target="external" href="/perl/ontology/search_term?id=GO:0008150">biological_n_n_process</a> where the function of the respective protein entry is required</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b><i><u>Cellular component:</u></i></b>&nbsp;_n_n_List of GO term(s) that identifies the localization of the protein entry_n_n_in the sub <a target="external" href="/perl/ontology/search_term?id=GO:0005575">cellular_n_n_component</a></font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b><i><u>Evidence:</u></i></b>&nbsp;_n_n_For the evidences the database uses:</font></font></li>_n_n__n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1>The <a target="external" href="http://www.ebi.ac.uk/interpro/">Interpro</a>_n_n_term as an evidence for the respective mapping of the GO term to the gene_n_n_product. The IDs will link to the <a target="external" href="http://www.ebi.ac.uk/interpro/">Interpro</a>_n_n_database.</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1>The literature (peer reviewed_n_n_publication) citing the respective mapping of the GO term to the gene product._n_n_The reference IDs will link them to the record listed in the <a target="external" href="/perl/pub_search">Gramene_n_n_Publication database</a>.</font></font></li>_n_n_</ul>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b><i><u>Evidence code:</u></i></b>&nbsp;_n_n_Lists the <a target="external" href="/plant_ontology/evidence_codes.html">evidence_n_n_code</a>, that was used in making the assertion on the GO-Interpro term_n_n_mapping (mainly <a target="external" href="/plant_ontology/evidence_codes.html#IEA">IEA</a>),_n_n_however the the GO-Interpro term mapping based on literature citation or_n_n_reviewed by the curator will carry an evidence code other than IEA.</font></font></li>_n_n_</ul>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Pfam:&nbsp;</b> Describes_n_n_the protein family to which the respective protein entry belongs to. Links_n_n_the Pfam ID to the <a target="external" href="http://www.sanger.ac.uk/Software/Pfam/index.shtml">Pfam_n_n_</a>database. The option available to view the list of rice protein database entries at Gramene, sharing this Pfam motif.</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Prosite:&nbsp;</b> Describes_n_n_the various prosite signatures the respective protein entry carries. The_n_n_Prosite IDs link to <a target="external" href="http://www.expasy.org/prosite/">Prosite</a>_n_n_	1
protein	Protein Search	database. The option available to view the list of rice protein database entries at Gramene, sharing this Prosite motif. The "residues from" section shows residue number in protein chain from where the Prosite domain starts and the amino acid sequence of domain in the protein. </font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Physiochemical features:</b>&nbsp;_n_n_Links the protein entry to the Expasy for analyses of physio-chemical features_n_n_analyzed by <a target="external" href="http://www.expasy.ch/tools/protparam.html">ProtParam</a>_n_n_tool.</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Plant Tissue/Cell type: _n_n_</b>Lists the localization of the protein entry in a plant, by way of using the Plant_n_n_Ontology (PO) term. Plant ontology being developed by <a target="external" href="http://www.arabidopsis.org">TAIR</a>_n_n_and <a target="external" href="/index.html">Gramene</a>, will describe the terms_n_n_of a plant at morphological and anatomical level except at the sub cellular_n_n_level (which is a part of Gene Ontology).</font></font></li>_n_n__n_n_<li>_n_n_<font face="Arial,Helvetica"><font size=-1><b>Keywords:</b>&nbsp; List_n_n_of keywords that are associated with the protein entry.</font></font></li>_n_n__n_n__n_n_</ul>_n_n_</ul>_n_n_</ul>_n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><b>Features:&nbsp; </b><font size=-1>The table provides the list of features. At present the only feature type available is the "transmembrane". More details_n_n_on how the predictions were generated is available at <a target="external" href="ftp://www.gramene.org/pub/gramene/protein/feature/Oryza_TMHMM_result.txt">FTP</a>._n_n_The table shows <b>Feature type / Residues (From-To)</b> suggesting the region on the protein chain / <b>Evidence</B> related to feature type and the <b>Evidence code</b>. For details on evidence code please follow the links as above._n_n_</font></font></li>_n_n_</ul>_n_n__n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><b>References Used for Curation:&nbsp; </b><font size=-1>List of all the references used for annotation of this protein. It also gives an option to search in Gramene Literature database for all the references that may be associated with this entry._n_n_</font></font></li>_n_n_</ul>_n_n__n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><b>Similarity to other proteins:&nbsp; </b><font size=-1>The_n_n_terms under this table links to the BLINK from the <a target="external" href="http://www.ncbi.nlm.nih.gov:80/Entrez/">NCBI</a>,_n_n_to find out the homologues / orthologues / proetins having similar 3D-structures_n_n_with the nearest relative in taxonomic term. It also links to the <a target="external" href="http://bsmir24.biochem.ucl.ac.uk/bsm/sas/">SAS</a> (Sequence Annotated by Structure)_n_n_database at University College London to identify similarity to protein_n_n_3D structure.</font></font></li>_n_n_</ul>_n_n_<ul>_n_n_<li>_n_n_<font face="Arial,Helvetica"><b>Comments:</b>&nbsp<font size=-1>Will carry the concise notes from curator's records, which is of interest_n_n_to the users community. Such as Expression pattern.</font></font></li>_n_n_</ul>_n_n__n_n_<font face="Arial,Helvetica"><font size=-1></font></font>_n_n_<p><br>_n_n_<hr SIZE=3 NOSHADE WIDTH="100%">_n_n_<center><font face="Arial,Helvetica"><font size=-1>Last modified on May 10, 2002</font></font></center>_n_n_	2
