This reports the protocol used to align the Maize_ESTcluster_TIGR features to Maize_BACs_20060126. Mon Feb 13 23:34:45 2006 Source of Maize_ESTcluster_TIGR : Downloaded from tigr with link ftp://ftp.tigr.org/pub/data/tgi/Zea_mays/ZMGI.release_15.zip Alignment procedure details --------------------------- 58582 Maize_ESTcluster_TIGR are aligned to Maize_BACs_20060126 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 : 12567 # unique Features these alignments represent: 8727 % of total features these alignments represent : 14.90 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 84 19 457 29 798 39 1053 49 1007 59 850 69 790 79 793 89 1146 90 175 91 203 92 269 93 317 94 334 95 419 96 514 97 563 98 559 99 835 100 1401 Alignments less than 95 % coverage are deleted # remaining Alignments : 3872 # unique Features these remaining alignments represent: 2820 % of total features these alignments represent : 4.81 % Gap distribution of the remaining features Gaps # alignments -------- -------- 1000 3025 2000 364 3000 162 4000 76 5000 49 6000 18 7000 22 8000 22 9000 16 10000 20 20000 41 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 3627 # unique Features these remaining alignments represent: 2656 % of total features these alignments represent : 4.53 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 12 95 177 96 287 97 370 98 685 99 1412 100 684 Frequency distribution of the remaining features # hits # features -------- -------- 1 2127 2 367 3 75 4 34 5 21 6 6 8 13 9 3 10 2 20 8 30 0 40 0 50 0 100 0 Features that hit more than four times are deleted. # remaining Alignments : 3222 # unique Features these remaining alignments represent: 2603 % of total features these alignments represent : 4.44 %