This reports the protocol used to align the Wheat_Marker features to tigrv4-genome. Fri Apr 14 11:48:34 2006 Source of Wheat_Marker : Downloaded from genbank with query ' txid4564[orgn] AND gbdiv_est[PROP]' Alignment procedure details --------------------------- 3670 Wheat_Marker 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 : 3640 # unique Features these alignments represent: 3565 % of total features these alignments represent : 97.14 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 39 150 90 200 624 250 672 300 603 350 523 400 445 450 314 500 194 550 96 600 33 650 7 700 0 750 0 800 0 10000 0 Alignments with matches less than 150 bp are deleted # remaining Alignments : 3529 # unique Features these remaining alignments represent: 3455 % of total features these alignments represent : 94.14 % Frequency distribution of the remaining features # hits # features -------- -------- 1 3386 2 64 3 5 4 0 5 0 6 0 8 0 9 0 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 3529 # unique Features these remaining alignments represent: 3455 % of total features these alignments represent : 94.14 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 0 50 0 60 1 70 26 80 250 90 2465 95 761 100 26 Following is the distribution of gaps Gaps # features -------- -------- 1000 2935 2000 388 3000 86 4000 36 5000 12 6000 9 7000 8 8000 2 9000 4 10000 3 Following is the final summary # alignments : 3529 # unique Features these alignments represent: 3455 % of total features these alignments represent : 94.14 %