This reports the protocol used to align the RiceAlta_BACend_OMAP features to tigrv4-genome. Fri Apr 14 17:03:02 2006 Source of RiceAlta_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OA_BBa' Alignment procedure details --------------------------- 128732 RiceAlta_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 : 145760 # unique Features these alignments represent: 110521 % of total features these alignments represent : 85.85 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 14618 150 16185 200 12487 250 12122 300 11339 350 10546 400 10341 450 11046 500 9944 550 9222 600 8129 650 7532 700 5514 750 3782 800 2022 10000 931 Alignments with matches less than 100 bp are filtered # remaining Alignments : 131415 # unique Features these remaining alignments represent: 98569 % of total features these alignments represent : 76.57 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 114685 2000 900 3000 386 4000 316 5000 185 6000 154 7000 139 8000 128 9000 115 10000 76 20000 778 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 116287 # unique Features these remaining alignments represent: 88290 % of total features these alignments represent : 68.58 % Frequency distribution of the remaining features # hits # features -------- -------- 1 77064 2 6672 3 1833 4 861 5 471 6 290 8 596 9 119 10 90 20 214 30 25 40 19 50 10 100 26 Features that hit more than thrice are deleted. # remaining Alignments : 95907 # unique Features these remaining alignments represent: 85569 % of total features these alignments represent : 66.47 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 0 30 14 40 104 50 281 60 1007 70 5677 80 10219 90 27055 100 51550 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 94691 # unique Features these remaining alignments represent: 84494 % of total features these alignments represent : 65.64 % Following is the final summary # alignments : 94691 # unique Features these alignments represent: 84494 % of total features these alignments represent : 65.64 %