This reports the protocol used to align the Maize_EST features to tigrv4-genome. Fri Apr 14 19:51:04 2006 Source of Maize_EST : from Gramene markers database, originally Downloaded from genbank with query ' txid4577[orgn] AND gbdiv_est[PROP]' Alignment procedure details --------------------------- 705163 Maize_EST 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 : 484738 # unique Features these alignments represent: 452339 % of total features these alignments represent : 64.15 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 55217 150 53581 200 60429 250 57680 300 56418 350 51253 400 48765 450 35411 500 24527 550 17953 600 10947 650 6568 700 3774 750 1583 800 449 10000 183 Alignments with matches less than 150 bp are deleted # remaining Alignments : 377288 # unique Features these remaining alignments represent: 350024 % of total features these alignments represent : 49.64 % Frequency distribution of the remaining features # hits # features -------- -------- 1 335502 2 9310 3 2165 4 1123 5 846 6 474 8 386 9 77 10 62 20 79 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 360617 # unique Features these remaining alignments represent: 346977 % of total features these alignments represent : 49.21 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 2 30 3 40 17 50 84 60 292 70 1737 80 23647 90 249355 95 81764 100 3716 Following is the distribution of gaps Gaps # features -------- -------- 1000 293205 2000 44180 3000 11590 4000 3117 5000 1709 6000 864 7000 546 8000 460 9000 249 10000 260 Following is the final summary # alignments : 360617 # unique Features these alignments represent: 346977 % of total features these alignments represent : 49.21 %