This reports the protocol used to align the Sorghum_GSS_Klein features to tigrv4-genome. Fri Apr 14 11:50:07 2006 Source of Sorghum_GSS_Klein : from Gramene markers database, originally These are from Patricia Klein Alignment procedure details --------------------------- 172 Sorghum_GSS_Klein 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 : 140 # unique Features these alignments represent: 139 % of total features these alignments represent : 80.81 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 17 150 29 200 18 250 24 300 15 350 14 400 10 450 3 500 4 550 1 600 4 650 1 700 0 750 0 800 0 10000 0 Alignments with matches less than 100 bp are filtered # remaining Alignments : 124 # unique Features these remaining alignments represent: 124 % of total features these alignments represent : 72.09 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 122 2000 0 3000 0 4000 1 5000 0 6000 1 7000 0 8000 0 9000 0 10000 0 20000 0 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 123 # unique Features these remaining alignments represent: 123 % of total features these alignments represent : 71.51 % Frequency distribution of the remaining features # hits # features -------- -------- 1 123 2 0 3 0 4 0 5 0 6 0 8 0 9 0 10 0 20 0 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 123 # unique Features these remaining alignments represent: 123 % of total features these alignments represent : 71.51 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 0 30 0 40 0 50 0 60 0 70 2 80 14 90 85 100 22 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 123 # unique Features these remaining alignments represent: 123 % of total features these alignments represent : 71.51 % Following is the final summary # alignments : 123 # unique Features these alignments represent: 123 % of total features these alignments represent : 71.51 %