This reports the protocol used to align the RiceMinuta_BACend_OMAP features to tigrv4-genome. Fri Apr 14 16:52:18 2006 Source of RiceMinuta_BACend_OMAP : from Gramene markers database, originally From genbank Nucleotide database with keyword 'OM__Ba' Alignment procedure details --------------------------- 169651 RiceMinuta_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 : 215500 # unique Features these alignments represent: 152250 % of total features these alignments represent : 89.74 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 10738 150 12209 200 14809 250 15844 300 16689 350 18006 400 18665 450 20002 500 20869 550 20730 600 19252 650 13729 700 8166 750 3868 800 1368 10000 556 Alignments with matches less than 100 bp are filtered # remaining Alignments : 204996 # unique Features these remaining alignments represent: 143532 % of total features these alignments represent : 84.60 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 179234 2000 1307 3000 642 4000 617 5000 276 6000 290 7000 208 8000 173 9000 301 10000 151 20000 1142 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 181800 # unique Features these remaining alignments represent: 128302 % of total features these alignments represent : 75.63 % Frequency distribution of the remaining features # hits # features -------- -------- 1 109994 2 10414 3 2799 4 1331 5 843 6 550 8 985 9 248 10 181 20 703 30 153 40 49 50 31 100 21 Features that hit more than thrice are deleted. # remaining Alignments : 139219 # unique Features these remaining alignments represent: 123207 % of total features these alignments represent : 72.62 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 1 30 10 40 70 50 260 60 894 70 4188 80 14951 90 47711 100 71134 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 138138 # unique Features these remaining alignments represent: 122243 % of total features these alignments represent : 72.06 % Following is the final summary # alignments : 138138 # unique Features these alignments represent: 122243 % of total features these alignments represent : 72.06 %