This reports the protocol used to align the Maize_EST features to Maize_BACs_20060126. Mon Feb 13 20:56:42 2006 Source of Maize_EST : Downloaded from genbank with query ' txid4577[orgn] AND gbdiv_est[PROP]' Alignment procedure details --------------------------- 417056 Maize_EST are aligned to Maize_BACs_20060126 using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets. Initial summary # alignments : 83967 # unique Features these alignments represent: 60542 % of total features these alignments represent : 14.52 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 0 19 149 29 2302 39 4050 49 3959 59 3693 69 4008 79 4319 89 6666 90 1171 91 1504 92 1876 93 2295 94 2684 95 3652 96 4891 97 6617 98 8703 99 8796 100 12629 Alignments less than 95 % coverage are deleted # remaining Alignments : 41687 # unique Features these remaining alignments represent: 29278 % of total features these alignments represent : 7.02 % Gap distribution of the remaining features Gaps # alignments -------- -------- 1000 36889 2000 2352 3000 1110 4000 326 5000 136 6000 57 7000 56 8000 233 9000 51 10000 128 20000 145 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 40677 # unique Features these remaining alignments represent: 28593 % of total features these alignments represent : 6.86 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 62 95 786 96 1817 97 5682 98 8680 99 14690 100 8960 Frequency distribution of the remaining features # hits # features -------- -------- 1 22181 2 4044 3 1245 4 308 5 459 6 126 8 147 9 22 10 11 20 34 30 11 40 3 50 1 100 1 Features that hit more than four times are deleted. # remaining Alignments : 35236 # unique Features these remaining alignments represent: 27778 % of total features these alignments represent : 6.66 %