This reports the protocol used to align the Rice_ESTcluster_TIGR features to tigrv4-genome. Fri Apr 14 12:25:53 2006 Source of Rice_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from TIGR at ftp://ftp.tigr.org/pub/data/tgi/Oryza_sativa/OGI.release_16.zip Alignment procedure details --------------------------- 36381 Rice_ESTcluster_TIGR 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 # alignments : 38815 # unique Features these alignments represent: 35830 % of total features these alignments represent : 98.49 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 0 19 24 29 16 39 44 49 120 59 417 69 443 79 587 89 959 90 153 91 173 92 201 93 246 94 331 95 411 96 550 97 835 98 1369 99 2868 100 29054 Alignments less than 95 % coverage are deleted # remaining Alignments : 34694 # unique Features these remaining alignments represent: 32374 % of total features these alignments represent : 88.99 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 18077 2000 6579 3000 4282 4000 2282 5000 1224 6000 683 7000 417 8000 245 9000 194 10000 116 20000 305 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 31220 # unique Features these remaining alignments represent: 29119 % of total features these alignments represent : 80.04 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 1 95 13 96 52 97 220 98 1043 99 12471 100 17420 Frequency distribution of the remaining features # hits # features -------- -------- 1 28513 2 360 3 98 4 40 5 22 6 14 8 19 9 5 10 6 20 27 30 4 40 6 50 2 100 2 Features that hit more than four times are deleted. # remaining Alignments : 29687 # unique Features these remaining alignments represent: 29011 % of total features these alignments represent : 79.74 %