This reports the protocol used to align the RiceCoarctata_BACend_OMAP features to tigrv4-genome. Fri Apr 14 17:18:54 2006 Source of RiceCoarctata_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OC__Ba' Alignment procedure details --------------------------- 195285 RiceCoarctata_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 : 154825 # unique Features these alignments represent: 128110 % of total features these alignments represent : 65.60 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 21084 150 11196 200 10519 250 9844 300 9684 350 9920 400 10046 450 10341 500 10855 550 11002 600 10845 650 9630 700 7707 750 5518 800 3684 10000 2950 Alignments with matches less than 100 bp are filtered # remaining Alignments : 134005 # unique Features these remaining alignments represent: 109868 % of total features these alignments represent : 56.26 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 129437 2000 746 3000 261 4000 189 5000 95 6000 119 7000 115 8000 93 9000 67 10000 62 20000 432 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 130633 # unique Features these remaining alignments represent: 107232 % of total features these alignments represent : 54.91 % Frequency distribution of the remaining features # hits # features -------- -------- 1 99591 2 3273 3 1072 4 883 5 609 6 284 8 1160 9 107 10 81 20 156 30 12 40 1 50 0 100 2 Features that hit more than thrice are deleted. # remaining Alignments : 109353 # unique Features these remaining alignments represent: 103936 % of total features these alignments represent : 53.22 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 3 30 31 40 132 50 521 60 2136 70 3779 80 6639 90 30055 100 66057 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 106850 # unique Features these remaining alignments represent: 101669 % of total features these alignments represent : 52.06 % Following is the final summary # alignments : 106850 # unique Features these alignments represent: 101669 % of total features these alignments represent : 52.06 %