This reports the protocol used to align the RiceAustraliensis_BACend_OMAP features to tigrv4-genome. Fri Apr 14 17:54:48 2006 Source of RiceAustraliensis_BACend_OMAP : from Gramene markers database, originally Downloaded from genbank nucleotide databse with keyword 'OA_ABa' Alignment procedure details --------------------------- 128599 RiceAustraliensis_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 : 167386 # unique Features these alignments represent: 106887 % of total features these alignments represent : 83.12 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 12077 150 11671 200 13174 250 10224 300 9778 350 9370 400 9931 450 11166 500 13031 550 13342 600 12568 650 11684 700 10161 750 8839 800 6391 10000 3979 Alignments with matches less than 100 bp are filtered # remaining Alignments : 155545 # unique Features these remaining alignments represent: 97697 % of total features these alignments represent : 75.97 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 129034 2000 547 3000 200 4000 217 5000 156 6000 190 7000 344 8000 184 9000 191 10000 148 20000 963 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 129998 # unique Features these remaining alignments represent: 81733 % of total features these alignments represent : 63.56 % Frequency distribution of the remaining features # hits # features -------- -------- 1 65357 2 8524 3 2753 4 1506 5 823 6 530 8 1240 9 176 10 158 20 474 30 78 40 69 50 26 100 18 Features that hit more than thrice are deleted. # remaining Alignments : 90664 # unique Features these remaining alignments represent: 76634 % of total features these alignments represent : 59.59 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 5 30 34 40 223 50 717 60 2653 70 10427 80 15781 90 23769 100 37055 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 87471 # unique Features these remaining alignments represent: 73872 % of total features these alignments represent : 57.44 % Following is the final summary # alignments : 87471 # unique Features these alignments represent: 73872 % of total features these alignments represent : 57.44 %