This reports the protocol used to align the Sorghum_ESTcluster_TIGR features to tigrv4-genome. Fri Apr 14 11:48:20 2006 Source of Sorghum_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from TIGR using link ftp://ftp.tigr.org/pub/data/tgi/Sorghum_bicolor/SBGI.release_8.zip Alignment procedure details --------------------------- 7996 Sorghum_ESTcluster_TIGR are aligned to tigrv4-genome using blat with blat parameters -minIdentity=50 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'CrossSpecies-Coding' data sets. Initial summary # alignments : 6912 # unique Features these alignments represent: 6266 % of total features these alignments represent : 78.36 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 441 150 549 200 689 250 698 300 771 350 843 400 613 450 549 500 387 550 300 600 247 650 188 700 133 750 88 800 85 10000 331 Alignments with matches less than 150 bp are deleted # remaining Alignments : 5932 # unique Features these remaining alignments represent: 5384 % of total features these alignments represent : 67.33 % Frequency distribution of the remaining features # hits # features -------- -------- 1 5172 2 106 3 16 4 29 5 26 6 21 8 5 9 4 10 3 20 2 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 5432 # unique Features these remaining alignments represent: 5294 % of total features these alignments represent : 66.21 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 3 50 2 60 5 70 44 80 354 90 3766 95 1168 100 90 Following is the distribution of gaps Gaps # features -------- -------- 1000 3979 2000 834 3000 328 4000 92 5000 41 6000 29 7000 7 8000 9 9000 9 10000 5 Following is the final summary # alignments : 5432 # unique Features these alignments represent: 5294 % of total features these alignments represent : 66.21 %