ensembl	EnsEMBL	<<ENSEMBL
To make the  sequence/feature/gene database and the contig viewer, gene viewer
and these help pages,
we started with version 1.00 of <a href="www.ensembl.org" target="external">EnsEMBL</a>, adapted it to using Oracle and
having a non-assembled genome, and added additional tracks, marker information, etc.
Thanks to Ewan Birney, James Stalker, Michelle Clamp, Arne Stabenau, and Nicole Redaschi of the EnsEMBL team
for helpful discussions.
ENSEMBL


helpview	Context-Sensitive Help	<<HELPVIEW
<p>
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>
<p>
<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.
</p>

These help pages were made by editing and adding to those supplied with <a href="HELP_ensembl_HELP">EnsEMBL</a>.
HELPVIEW



seqentryview	Clone/Contig viewer	<<SEQENTRYVIEW
<p>"SeqentryView" allows you to view and dump the contigs that make up a clone.</p>

<p>The top of the page gives the Clone identifier(Genbank Accession),
along with the Contig identifier. Below that is the Clone name and 
sequencing status. </p>

<p>Below the page header is a table showing a graphical display for this Contig.
The image is similar to those in "ContigView" (see <a href="HELP_contigview_HELP">help on "ContigView"</a>),
in that you can click on the features displayed to get more information.
It does not display ESTs.</p>

<p>If you wish to see all contigs in a clone, click on the "View all #
contigs" link at the top of the page. Alternatively, click on "contig
map" to get the "ContigView" page for this region</p>

<p>Under each contig image is a "Dump this region" link. Clicking on
this will take you to a page where you can configure the
<a href="HELP_dumpcfgview_HELP">flatfile dumping</a> of that contig. A
similar link below enables you to dump the entire clone.</p>

<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>
SEQENTRYVIEW

browser	Navigation bar Search / "Class Browser" / "Search the Gramene Database"	<<BROWSER
<p>Search the Acedb database which Gramene inherited from RiceGenes.
Also, <a href="/newsletters/rice_genetics/">Rice Genetics Newsletters</a> and Rice Genomic Newsletters.
'*' is a wildcard matching any sequence of characters.
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>.
</p>
<p>
To do an unrestricted text search on the Acedb database , check the
Detailed search (long) box and choose "Anything".
For a more structured search, use 
<a href="/gramene/searches/query" target="external">Acedb Query</a>
</p>
<p>Help on the contents of Gramene's Acedb database is available
<a href="http://www.gramene.org/gramene/searches/query?query=find%20HELP" target="external">here</a>.</p>
BROWSER

search	Sequence Database Search	<<SEARCH
<p>The search box at the top of each Gramene Ensembl page allows you to
search the whole sequence database ("Find 'All' ") or restrict the
search to a specific identifier present in the sequence database.  Use
"Find 'Object in acedb'" to search the <a href="HELP_browser_HELP">Acedb database</a> 
instead of the Sequence Database.
</p>
<p align="center">
<img src="IMG_unisearch_box.png_IMG" alt="search box"></p>

<h4>Restricted Search</h4>
<p>Select the type of identifier you are looking for from the drop-down
list to the left of the search box (Gene, Contig, Clone, BAC end,
Protein, Map marker) and type the identifier into the search box.
Use "*" as a wildcard.
"Protein" searches the Protein database, not the Sequence database.
Use <a href="HELP_protein_HELP">protein_search</a> to search the
Protein database in depth.<br>
Click the <img src="/gfx/lookup.gif" align="absmiddle" alt="search">
<br>There are context-type-sensitive examples shown to the right end of the box.
</p>

<h4>Find 'All'</h4>
<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>
</p>

<h4>Search Results Page</h4>
<p>
If you searched for a specific type of identifier by selecting it from
the search drop-down box, e.g. "Gene", then you will see a page of
results for that type.
</p>
<p>
Each search result is a link to a page giving more detail.
If there is only one hit you will be taken directly to this entry.
For BAC ends, the link goes to a <a href="HELP_contigview_HELP">contigview</a> 
page which displays the BAC end hit to the genome in context.  You can
go to the Genbank record for the BAC end from there.
</p>                       
SEARCH


contigview	Sequence Contig Displays	<<CONTIGVIEW
<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>

<p>
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>
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.
</p>

<h3>Overview</h3>

<p align="center">
<img src="/gfx/buttons/changefeatures.png" alt="comment"></p>
<p>
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).
</p>
<p>
The individual contigs are shown in alternating dark and light blue.  A horizontal line indicates a gap in the sequence assembly.</p>

<p align="center">
<img src="IMG_contigviewtop.png_IMG" alt="comment">
</p>

<p>
Markers are indicated in magenta and cyan (for ssr's) under the contig map.  Red boxes represent genes. 
BAC ends are green. 
Rice ESTs are represented in red: each exon is a box joined by lines above and below.
 ESTs from other species are shown similarly in shades of yellow and orange.
At present, the only genes shown are those that were annotated by the clone's submitter.
If the gene is in SPTREMBL, its name there will be shown, otherwise an arbitray sequential name (Gene1, Gene2, ... )
Above the contig map a small scale bar is given.  </p>
<p>
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>

<h3>Navigator Buttons</h3>
<p align="center">
<img src="/gfx/buttons/dump.gif" alt="comment"></p>
<p>
This dump button allows you to dump the specified region as a flat file (see <a href="HELP_dumpcfgview_HELP">Flatfile Dumping</a>).
</p>


<p align="center">
<img src="/gfx/buttons/win_left.gif" alt="comment">
<img src="/gfx/buttons/win_right.gif" alt="comment">
</p>
<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>

<p align="center">
<img src="IMG_zoom.gif_IMG" alt="comment">
</p>
<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>

<p align="center">
<img src="/gfx/buttons/changefeatures.png" alt="comment"></p>
<p>
This button allows you to configure the look of the "Detailed View" (see <a href="HELP_config_HELP">Configuration</a> for more details).
</p>

<h3>Detailed View</h3>
<p>
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.  

Mouseover and "tooltip" text will show the feature's name and a link to more detailed information where available.</p>
<p align="center">
<img src="IMG_contigviewbottom.jpg_IMG" alt="comment"></p>

<p>
<b>DNA (contigs)</b><br>
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>".

<p>
<b>Transcripts</b><br>
"Detailed View" does not display genes as such but rather their
transcripts.  Ensembl considers genes as a collection of exons - from
which there may be many transcripts.  At present the only transcripts
in our database are those annotated by the sequencing centers, and are
red as if they were
"known transcripts" generated by Ensembl.
"External transcripts" would be either green (curated as gene) or gray
(curated as pseudogene), 
Ensembl "novel transcripts" would be black.  If there are
several transcripts at the same point on the sequence then that gene
has been assessed as producing multiple transcripts (displayed on
different lines).  
Mouseover on a transcript
</p>
<p align="center">
<img src="IMG_contigviewprotein.jpg_IMG" alt="comment"></p>

<p>
will produce a menu with the name of the transcript 
(the SwissProt id of any corresponding protein,
otherwise the 
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein" target="external">
Genbank Protein
Database</a> id, or a Gramene id)
at the top:<br>

<ul>
<li><b>Transcript information</b> will take you to "<a href="HELP_geneview_HELP">GeneView</a>", providing data on the predicted gene</li>

<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>

<li><b>Protein sequence (FASTA)</b> will take you to "DumpView", showing the peptide sequence in FASTA format.</li>


<li><b>cDNA sequence</b> will take you to "DumpView", showing the CDNA sequence for this transcript in FASTA format.</li>
</ul>
</p>

<p>
The following features are strand independent and are shown at the bottom of the "Detailed View".
</p>

<p>
<b>SSR Marker</b><br>
These are <a href="/documentation/bac_ssr.txt" target="external">Cornell Rice SSRs</a>.
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>.
</p>

<p>
<b>Marker Sequence Tag</b><br>
These are <a href="/documentation/bac_marker_documentation.txt" target="external">JRGP/Cornell Markers</a>.
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> 
or the sequence of the marker in Genbank.
</p>

<p>
<BAC Ends>
These are <a href="/documentation/bac_bacend_documentation.txt" target="external">CUGI Bacends</a>.
Mouseover and "tooltip" text will show the id of this marker and the
option to view the sequence of the BAC end in Genbank.
</p>

<p>
<b>ESTs</b><br>
These tracks show <a href="/documentation/index.html#est" target="external">alignments to the rice genome</a> of rice and other grain mRNA
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>.  Mouseover and "tooltip" text will show the Genbank id and the option to view this Genbank entry.
</p>

<p>
<b>Repeats</b><br>
This indicates a region of repetitive sequence.
</p>

<p>
<b>%GC</b><br>
The plot shows you the relative GC content.
</p>

<h3>Navigator Bar</h3>
<p>
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.
</p>

<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>

</p>
CONTIGVIEW

protview	Ensembl Protein Report	<<PROTVIEW
<p>"ProteinView" provides information about a particular protein in the 
sequence database.  Proteins in SwissProt and curated proteins have a 
<a href="HELP_protein_HELP">more detailed page</a> available.  </p>

<p>The summary table at the top of the report provides the following data about the protein:
<ul>
	<li><b>Gramene Protein ID</b> - the Gramene protein identifier.</li>
	<li><b>Gramene Gene</b> - the corresponding Gramene gene identifier.</li>
	<li><b>Description</b> - the name of the protein.</li>
	<li><b>Prediction Method</b> - how the protein was predicted.</li>
	<li><b>Protein structure</b> - a map showing protein domains (e.g. Pfam) and  protein features (transmembrane, low complexity and coli regions).</li>
</ul>
<p>Below the summary table are a series of detailed tables describing the protein</p>
<ul>
	<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>
</ul>

<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>


PROTVIEW




markerview	Map Marker Information	<<MARKERVIEW
<p>"MarkerView" displays information about a particular map marker.</p>
<p>First, a link to the page for this 
<a href="/gramene/generic/tree?name=CLICK_HERE_FOR_Marker_Info&class=LongText" target="external">marker in the acedb database</a> is given.
If the marker has a sequency entry in Genbank, a link to that is given also.</p>
<p>The table on this page shows information about the sequenced
clone(s) to which the marker is mapped, including the position in the
clone and links to view or download the clone.  This table is omitted if
this marker is not currently mapped to any sequenced clone(s).
</p>




<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>
MARKERVIEW


dumpcfgview	Flatfile Dumping	<<DUMPCFGVIEW
<p>From "ContigView" etc, clicking on the button "view text" brings you to flatfile dumping</p>

<img src="/gfx/buttons/dump.gif" alt="Flatfile dumping button">

<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>

<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>

<p>You specify the type of feature, the feature id, and the type of output you require. For DNA-type features you can also specify a number of "context" basepairs to show either side of the chosen feature.</p>

<img src="IMG_dumpcfgview_feature_annot.gif_IMG" alt="comment">

<p>The specified region is generated dynamically from the sequence
database, and then sent to your browser in the format you chose.  <em>Note
that the 'Dump a Region' tab is not currently active because the rice
genome is not assembled.</em></p>

DUMPCFGVIEW


blastp	How do I find proteins similar to my protein sequence?	<<BLASTP
<OL>

<LI>Follow the "Blast Search" link on the Gramene navigation bar or just follow the link below.</LI>

<LI><A HREF='/gramene/searches/blast' target="external" class="grey2">Run similarity search on the Gramene BLAST Server</A>. 
just paste in your sequence and choose the appropriate options. Choose 
'Rice Proteins' as the database and blastp as the program or one of the
EST databases and tblastn as the program.
The 'Run BLAST' button submits your
sequence to the BLAST server. 
See <a href="HELP_blast_HELP">here</a> for more information.</LI>

<LI>The blast results contain hyperlinks to take you to the sequence you hit.</LI>
</OL>
BLASTP




missinggene	What if a gene appears to be incorrectly positioned in the genome?	<<MISSINGGENE
At present, all genes in the Gramene database are those annotated by the 
sequencing sites.  Many clones are not annotated.  Perhaps the gene is 
duplicated and the place you expect it to be has not yet been sequenced
and annotated.  This will become clearer in the future--we plan to have
an automated annotation of the whole sequenced genome.
MISSINGGENE


config	Customising 'Contigview Windows'	<<CONFIG
<p>
This table allows you to change the configuration of the "Overview" 
in "<a href="HELP_contigview_HELP">ContigView</a>" &#151;
if
you clicked the upper "Change Features" button &#151; or of the "Detailed
View" 
if you clicked
the lower one.  It gives you the option to turn on or off the
individual features (e.g. BAC end) and change the colours according to
your preferences (not possible for 'Transcript' and '%GC').<br>
Overlapping features (e.g. ESTs) can be separated by setting the depth to 'expanded' (default setting). 
</p>
<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>
<p>
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.
<br>Use <img src="IMG_reset.gif_IMG" align="absmiddle" alt="Help"> to get the default configuration. 
</p>
CONFIG

geneview	Ensembl Gene Report	<<GENEVIEW
<p>"GeneView" provides detailed information about a particular Gramene gene.</p>

<p>The summary table at the top of the report provides the following data about the gene:
<ul>
	<li><b>Ensembl gene ID</b> - the Gramene gene identifier.</li>
	<li><b>Genome Location</b> - the chromosome containing this gene with a link to "<a href="HELP_contigview_HELP">ContigView</a>".</li>
	<li><b>Description</b> - a short description of the gene.</li>
	<li><b>Predicted Transcripts</b> - a list of predicted
	transcripts for this gene with links to the transcript
	structure below and to "<a href="HELP_protview_HELP">ProteinView</a>". 
	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>
	<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.
</ul>
<p>A <a href="HELP_dumpcfgview_HELP">text dump</a> of the gene is available.</p>

<p>Below the summary table are a series of detailed tables describing the gene's predicted transcripts, sequence information, exons, and splice-sites.</p>

<p>The Sequence Information table has links to Transcript Sequence ("cDNA"), which provides the cDNA sequence for the transcript.</p>

<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>
GENEVIEW

SeqTable.cgi	Rice BAC/PAC Sequence Information	<<SEQTABLE
<p>
This page shows all sequenced Clones on a Rice Chromosome.
<ul>
<li>The clone names in the first column are links to the Gramene
<a href="HELP_contigview_HELP">"ContigView"</a> page for the clone.
<li>The Sequencing Site abbreviations link to the site's home page.
<li>The DNA length links to a FASTA file (at Genbank).
<li>The Accession number links to the Genbank entry for this clone.
</ul>
You may click on any column heading(except Fragments) to sort the table by that column,
or reverse the sort.
Sorting by HTG Phase implies the reverse sorting by number of fragments.
So Sorting from highest to lowest Phase (the default) implies sorting from least to most 
fragments within that (and annotated clones before unannotated).
</p>
SEQTABLE



maps	Genetic & Comparative Maps	@http://www.gramene.org/maps/help
protein	Protein Search	@http://www.gramene.org/documentation/protein_help.html
blast	Blast Search	@http://www.gramene.org/documentation/blast_help.html


vocabulary	Controlled Vocabulary Database	@http://www.gramene.org/documentation/ontology_help.html
vocabularysubmission	Controlled vocabulary online submission form	@http://www.gramene.org/documentation/cvo_help.html

mutantsubmission	Mutant online submission form	@http://www.gramene.org/documentation/mutant_help.html

mapviewer	Map Viewer Correspondences	@http://www.gramene.org/documentation/map_viewer_correspondences.html





