This reports the protocol used to align the Wheat_ArrayConsensus_Affy61K features to tigrv4-genome. Fri Apr 14 12:02:14 2006 Source of Wheat_ArrayConsensus_Affy61K : Downloaded from Affymetrix website Alignment procedure details --------------------------- 61115 Wheat_ArrayConsensus_Affy61K 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 : 32940 # unique Features these alignments represent: 30225 % of total features these alignments represent : 49.46 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 4442 150 4413 200 4506 250 3993 300 3201 350 2485 400 1939 450 1396 500 983 550 815 600 643 650 518 700 554 750 447 800 386 10000 2219 Alignments with matches less than 150 bp are deleted # remaining Alignments : 24182 # unique Features these remaining alignments represent: 22043 % of total features these alignments represent : 36.07 % Frequency distribution of the remaining features # hits # features -------- -------- 1 21146 2 470 3 107 4 81 5 96 6 92 8 36 9 6 10 5 20 4 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 22407 # unique Features these remaining alignments represent: 21723 % of total features these alignments represent : 35.54 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 1 30 0 40 3 50 10 60 34 70 171 80 1438 90 13902 95 6118 100 730 Following is the distribution of gaps Gaps # features -------- -------- 1000 16183 2000 3104 3000 1418 4000 636 5000 253 6000 121 7000 96 8000 62 9000 37 10000 38 Following is the final summary # alignments : 22407 # unique Features these alignments represent: 21723 % of total features these alignments represent : 35.54 %