This reports the protocol used to align the Rice_EST features to tigrv4-genome. Mon Apr 17 15:31:38 2006 Source of Rice_EST : from Gramene markers database, originally Downloaded from Genbank with query 'txid4530[orgn] AND gbdiv_est[PROP] Alignment procedure details --------------------------- 1274663 Rice_EST are aligned to tigrv4-genome 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 # aligments : 1310558 # unique Features these alignments represent: 1215951 % of total features these alignments represent : 95.39 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 1 19 211 29 1126 39 2677 49 4521 59 10055 69 17380 79 22534 89 54857 90 12561 91 14733 92 19170 93 24271 94 33034 95 43478 96 57253 97 76841 98 101990 99 165509 100 648349 Alignments less than 95 % coverage are deleted # remaining Aligments : 1050919 # unique Features these represent alignments represent: 980222 % of total features these alignments represent : 76.90 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 909693 2000 101381 3000 25253 4000 7916 5000 2607 6000 1220 7000 821 8000 383 9000 280 10000 219 20000 719 Alignments with gaps > 4000 bp are deleted # remaining Aligments : 1044243 # unique Features these represent alignments represent: 973921 % of total features these alignments represent : 76.41 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 118 95 1893 96 8316 97 22781 98 72158 99 464285 100 474692 Frequency distribution of the remaining features # hits # features -------- -------- 1 950535 2 12690 3 1991 4 1433 5 1154 6 1128 8 4281 9 464 10 67 20 108 30 15 40 14 50 11 100 16 Features that hit more than four times are deleted. # remaining Aligments : 987620 # unique Features these represent alignments represent: 966649 % of total features these alignments represent : 75.84 %