This reports the protocol used to align the Wheat_ESTcluster_TIGR features to tigrv4-genome. Fri Apr 14 12:03:04 2006 Source of Wheat_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from the TIGR using link ftp://ftp.tigr.org/pub/data/tgi/Triticum_aestivum/TAGI.release_9.zip Alignment procedure details --------------------------- 44954 Wheat_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 : 31860 # unique Features these alignments represent: 30008 % of total features these alignments represent : 66.75 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 2584 150 2607 200 2831 250 2968 300 2859 350 2801 400 2669 450 2183 500 1727 550 1439 600 1174 650 939 700 794 750 621 800 590 10000 3074 Alignments with matches less than 150 bp are deleted # remaining Alignments : 26727 # unique Features these remaining alignments represent: 25186 % of total features these alignments represent : 56.03 % Frequency distribution of the remaining features # hits # features -------- -------- 1 24349 2 556 3 99 4 55 5 64 6 36 8 23 9 4 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 25758 # unique Features these remaining alignments represent: 25004 % of total features these alignments represent : 55.62 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 1 40 3 50 14 60 27 70 219 80 2047 90 17554 95 5515 100 378 Following is the distribution of gaps Gaps # features -------- -------- 1000 17438 2000 4174 3000 1913 4000 779 5000 354 6000 158 7000 122 8000 77 9000 48 10000 43 Following is the final summary # alignments : 25758 # unique Features these alignments represent: 25004 % of total features these alignments represent : 55.62 %