This reports the protocol used to align the Millet_EST features to tigrv4-genome. Fri Apr 14 11:43:50 2006 Source of Millet_EST : from Gramene markers database, originally Downloaded from genbank with query ' Pennisetum glaucum AND gbdiv_est[PROP]' Alignment procedure details --------------------------- 3519 Millet_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 : 2513 # unique Features these alignments represent: 1806 % of total features these alignments represent : 51.32 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 290 150 256 200 360 250 213 300 229 350 206 400 203 450 181 500 138 550 102 600 95 650 67 700 61 750 74 800 26 10000 12 Alignments with matches less than 150 bp are deleted # remaining Alignments : 1970 # unique Features these remaining alignments represent: 1367 % of total features these alignments represent : 38.85 % Frequency distribution of the remaining features # hits # features -------- -------- 1 1229 2 30 3 12 4 9 5 14 6 8 8 60 9 5 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 1325 # unique Features these remaining alignments represent: 1271 % of total features these alignments represent : 36.12 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 0 50 1 60 2 70 9 80 66 90 789 95 415 100 43 Following is the distribution of gaps Gaps # features -------- -------- 1000 1122 2000 142 3000 25 4000 12 5000 1 6000 2 7000 7 8000 0 9000 1 10000 0 Following is the final summary # alignments : 1325 # unique Features these alignments represent: 1271 % of total features these alignments represent : 36.12 %