This reports the protocol used to align the RiceBrachyantha_BACend_OMAP features to tigrv4-genome. Fri Apr 14 12:24:15 2006 Source of RiceBrachyantha_BACend_OMAP : from Gramene markers database, originally Downloaded from Genbank with 'Brachyantha' as keyword Alignment procedure details --------------------------- 67364 RiceBrachyantha_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 : 68274 # unique Features these alignments represent: 52014 % of total features these alignments represent : 77.21 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 9215 150 6468 200 5179 250 4865 300 4770 350 4259 400 4521 450 4422 500 4368 550 4386 600 4220 650 4028 700 3522 750 2298 800 1269 10000 484 Alignments with matches less than 100 bp are filtered # remaining Alignments : 59193 # unique Features these remaining alignments represent: 44396 % of total features these alignments represent : 65.90 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 53135 2000 214 3000 72 4000 77 5000 61 6000 39 7000 32 8000 42 9000 53 10000 30 20000 266 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 53498 # unique Features these remaining alignments represent: 40136 % of total features these alignments represent : 59.58 % Frequency distribution of the remaining features # hits # features -------- -------- 1 36002 2 1873 3 644 4 416 5 275 6 142 8 511 9 47 10 53 20 138 30 18 40 2 50 5 100 10 Features that hit more than thrice are deleted. # remaining Alignments : 41680 # unique Features these remaining alignments represent: 38519 % of total features these alignments represent : 57.18 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 1 30 9 40 19 50 70 60 310 70 746 80 2219 90 15824 100 22482 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 41317 # unique Features these remaining alignments represent: 38200 % of total features these alignments represent : 56.71 % Following is the final summary # alignments : 41317 # unique Features these alignments represent: 38200 % of total features these alignments represent : 56.71 %