This reports the protocol used to align the Barley_EST features to tigrv4-genome. Fri Apr 14 18:21:06 2006 Source of Barley_EST : from Gramene markers database, originally Downloaded from genbank with query ' txid4512[orgn] AND gbdiv_est[PROP]' Alignment procedure details --------------------------- 419250 Barley_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 : 358211 # unique Features these alignments represent: 297320 % of total features these alignments represent : 70.92 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 27592 150 32401 200 38657 250 39526 300 40430 350 39930 400 38263 450 32084 500 22214 550 17091 600 13752 650 8785 700 4193 750 1761 800 1053 10000 479 Alignments with matches less than 150 bp are deleted # remaining Alignments : 298931 # unique Features these remaining alignments represent: 241622 % of total features these alignments represent : 57.63 % Frequency distribution of the remaining features # hits # features -------- -------- 1 219547 2 9281 3 3775 4 3939 5 1436 6 1148 8 2254 9 192 10 37 20 13 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 249434 # unique Features these remaining alignments represent: 232603 % of total features these alignments represent : 55.48 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 1 40 9 50 32 60 368 70 1300 80 13301 90 159040 95 68250 100 7133 Following is the distribution of gaps Gaps # features -------- -------- 1000 202277 2000 31304 3000 6923 4000 2168 5000 905 6000 373 7000 590 8000 268 9000 132 10000 229 Following is the final summary # alignments : 249434 # unique Features these alignments represent: 232603 % of total features these alignments represent : 55.48 %