This reports the protocol used to align the Maize_ESTcluster_TIGR features to tigrv4-genome. Fri Apr 14 11:58:56 2006 Source of Maize_ESTcluster_TIGR : from Gramene markers database, originally Downloaded from tigr with link ftp://ftp.tigr.org/pub/data/tgi/Zea_mays/ZMGI.release_15.zip Alignment procedure details --------------------------- 31375 Maize_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 : 23095 # unique Features these alignments represent: 21888 % of total features these alignments represent : 69.76 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 2062 150 1980 200 2370 250 2231 300 2062 350 1901 400 1807 450 1417 500 1214 550 935 600 754 650 568 700 571 750 475 800 384 10000 2364 Alignments with matches less than 150 bp are deleted # remaining Alignments : 19091 # unique Features these remaining alignments represent: 18155 % of total features these alignments represent : 57.86 % Frequency distribution of the remaining features # hits # features -------- -------- 1 17698 2 294 3 47 4 38 5 29 6 24 8 11 9 4 10 7 20 3 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 18427 # unique Features these remaining alignments represent: 18039 % of total features these alignments represent : 57.49 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 11 50 10 60 32 70 150 80 1488 90 13542 95 3008 100 186 Following is the distribution of gaps Gaps # features -------- -------- 1000 12332 2000 3139 3000 1502 4000 580 5000 290 6000 128 7000 74 8000 50 9000 31 10000 17 Following is the final summary # alignments : 18427 # unique Features these alignments represent: 18039 % of total features these alignments represent : 57.49 %