This reports the protocol used to align the Wheat_ESTcluster_TIGR features to Maize_BACs_20060126. Mon Feb 13 16:29:04 2006 Source of Wheat_ESTcluster_TIGR : Downloaded from the TIGR using link ftp://ftp.tigr.org/pub/data/tgi/Triticum_aestivum/TAGI.release_9.zip Alignment procedure details --------------------------- 128088 Wheat_ESTcluster_TIGR are aligned to Maize_BACs_20060126 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 : 15247 # unique Features these alignments represent: 11238 % of total features these alignments represent : 8.77 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 3960 150 2083 200 1855 250 1432 300 1288 350 1243 400 1101 450 754 500 525 550 389 600 152 650 84 700 75 750 44 800 50 10000 212 Alignments with matches less than 150 bp are deleted # remaining Alignments : 9242 # unique Features these remaining alignments represent: 6235 % of total features these alignments represent : 4.87 % Frequency distribution of the remaining features # hits # features -------- -------- 1 5111 2 515 3 123 4 54 5 168 6 216 8 46 9 0 10 0 20 1 30 1 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 6510 # unique Features these remaining alignments represent: 5749 % of total features these alignments represent : 4.49 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 9 50 15 60 54 70 154 80 749 90 3265 95 1378 100 886 Following is the distribution of Gaps Gaps # features -------- -------- 1000 5617 2000 426 3000 217 4000 81 5000 29 6000 29 7000 16 8000 15 9000 16 10000 7 Following is the final summary # alignments : 6510 # unique Features these alignments represent: 5749 % of total features these alignments represent : 4.49 %