This reports the protocol used to align the nonRice_MarkerRFLP features to tigrv4-genome. Fri Apr 14 11:43:43 2006 Source of nonRice_MarkerRFLP : These are obtained from Cornell Alignment procedure details --------------------------- 1897 nonRice_MarkerRFLP 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 : 902 # unique Features these alignments represent: 856 % of total features these alignments represent : 45.12 % The length of the matches are distributed as follows Hit_Length # alignments -------- -------- 100 187 150 139 200 169 250 95 300 85 350 58 400 46 450 47 500 27 550 16 600 10 650 4 700 4 750 4 800 1 10000 10 Alignments with matches less than 150 bp are deleted # remaining Alignments : 578 # unique Features these remaining alignments represent: 545 % of total features these alignments represent : 28.73 % Frequency distribution of the remaining features # hits # features -------- -------- 1 523 2 18 3 1 4 1 5 0 6 2 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 : 562 # unique Features these remaining alignments represent: 542 % of total features these alignments represent : 28.57 % % Identity distribution of the remaining features % Identity # features -------- -------- 10 0 20 0 30 0 40 0 50 1 60 2 70 6 80 41 90 383 95 123 100 6 Following is the distribution of gaps Gaps # features -------- -------- 1000 507 2000 31 3000 10 4000 3 5000 1 6000 1 7000 0 8000 1 9000 0 10000 1 Following is the final summary # alignments : 562 # unique Features these alignments represent: 542 % of total features these alignments represent : 28.57 %