This reports the protocol used to align the Barley_ArrayExemplar_Affy22K features to tigrv4-genome. Fri Apr 14 11:44:00 2006 Source of Barley_ArrayExemplar_Affy22K : Barley GeneChip exemplars were obtained from Roger Wise and Stacy Turner.\nThey are described in \nthis publication. Alignment procedure details --------------------------- 21239 Barley_ArrayExemplar_Affy22K 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 : 14167 # unique Features these alignments represent: 13372 % of total features these alignments represent : 62.96 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 1237 150 1116 200 1293 250 1236 300 1217 350 995 400 923 450 800 500 668 550 556 600 549 650 440 700 397 750 348 800 291 10000 2101 Alignments with matches less than 150 bp are deleted # remaining Alignments : 11838 # unique Features these remaining alignments represent: 11190 % of total features these alignments represent : 52.69 % Frequency distribution of the remaining features # hits # features -------- -------- 1 10891 2 178 3 46 4 22 5 13 6 10 8 20 9 10 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 11385 # unique Features these remaining alignments represent: 11115 % of total features these alignments represent : 52.33 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 2 50 7 60 15 70 98 80 993 90 8248 95 1898 100 124 Following is the distribution of gaps Gaps # features -------- -------- 1000 6967 2000 2108 3000 1100 4000 470 5000 207 6000 104 7000 65 8000 43 9000 34 10000 14 Following is the final summary # alignments : 11385 # unique Features these alignments represent: 11115 % of total features these alignments represent : 52.33 %