This reports the protocol used to align the Rice_ArrayOligo_Yale58K features to tigrv4-genome. Fri Jun 30 20:46:45 2006 Source of Rice_ArrayOligo_Yale58K : These are Rice Gene Micro Array Oligos from Tim Nelson's lab at Yale University, this oligo set is derived from a combination of indica and japonica sequence. Alignment procedure details --------------------------- 58404 Rice_ArrayOligo_Yale58K 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 : 72721 # unique Features these alignments represent: 53906 % of total features these alignments represent : 92.30 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 10 0 20 0 30 25 40 300 Alignments with matches less than 10 bp are deleted # remaining Alignments : 72721 # unique Features these remaining alignments represent: 53906 % of total features these alignments represent : 92.30 % Frequency distribution of the remaining features # hits # features -------- -------- 1 50516 2 1873 3 493 4 219 5 139 6 96 8 148 9 42 10 34 20 179 30 69 40 24 50 19 100 24 Features that hit more than thrice are deleted. # remaining Alignments : 55741 # unique Features these remaining alignments represent: 52882 % of total features these alignments represent : 90.55 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 0 50 0 60 0 70 1 80 6 90 271 95 2173 100 53290 Following is the distribution of gaps Gaps # features -------- -------- 1000 55554 2000 105 3000 24 4000 10 5000 5 6000 5 7000 4 8000 3 9000 1 10000 1 Following is the final summary # alignments : 55741 # unique Features these alignments represent: 52882 % of total features these alignments represent : 90.55 %