This reports the protocol used to align the RicePunctata_BACend_OMAP features to tigrv4-genome. Fri Apr 14 14:50:14 2006 Source of RicePunctata_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OP__Ba' Alignment procedure details --------------------------- 68384 RicePunctata_BACend_OMAP 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-Genomic' data sets. Initial summary # alignments : 93229 # unique Features these alignments represent: 64422 % of total features these alignments represent : 94.21 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 3078 150 3455 200 4537 250 4906 300 5247 350 5375 400 5237 450 5511 500 6103 550 7120 600 7876 650 9213 700 9054 750 7544 800 5224 10000 3749 Alignments with matches less than 100 bp are filtered # remaining Alignments : 90206 # unique Features these remaining alignments represent: 61844 % of total features these alignments represent : 90.44 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 74647 2000 897 3000 429 4000 345 5000 288 6000 204 7000 179 8000 112 9000 77 10000 90 20000 668 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 76318 # unique Features these remaining alignments represent: 53061 % of total features these alignments represent : 77.59 % Frequency distribution of the remaining features # hits # features -------- -------- 1 45483 2 3919 3 1257 4 650 5 419 6 260 8 483 9 109 10 109 20 274 30 43 40 20 50 22 100 13 Features that hit more than thrice are deleted. # remaining Alignments : 57092 # unique Features these remaining alignments represent: 50659 % of total features these alignments represent : 74.08 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 0 30 2 40 12 50 70 60 340 70 1325 80 4895 90 17126 100 33322 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 56734 # unique Features these remaining alignments represent: 50349 % of total features these alignments represent : 73.63 % Following is the final summary # alignments : 56734 # unique Features these alignments represent: 50349 % of total features these alignments represent : 73.63 %