This reports the protocol used to align the Maize_FSTMu features to tigrv4-genome. Fri Apr 14 16:28:33 2006 Source of Maize_FSTMu : Downloaded from genbank with query ' (txid4577[ORGN] AND Walbot[AUTH] AND RescueMu[TITL])' Alignment procedure details --------------------------- 178124 Maize_FSTMu 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 : 62399 # unique Features these alignments represent: 50910 % of total features these alignments represent : 28.58 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 23197 150 13403 200 10804 250 5133 300 5740 350 1534 400 1122 450 583 500 458 550 266 600 101 650 54 700 4 750 0 800 0 10000 0 Alignments with matches less than 100 bp are filtered # remaining Alignments : 39379 # unique Features these remaining alignments represent: 31427 % of total features these alignments represent : 17.64 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 39146 2000 3 3000 3 4000 23 5000 35 6000 5 7000 8 8000 1 9000 2 10000 2 20000 23 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 39175 # unique Features these remaining alignments represent: 31261 % of total features these alignments represent : 17.55 % Frequency distribution of the remaining features # hits # features -------- -------- 1 29297 2 644 3 214 4 234 5 294 6 125 8 93 9 45 10 28 20 287 30 0 40 0 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 31227 # unique Features these remaining alignments represent: 30155 % of total features these alignments represent : 16.93 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 0 30 8 40 11 50 39 60 84 70 301 80 3754 90 17191 100 9839 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 31092 # unique Features these remaining alignments represent: 30035 % of total features these alignments represent : 16.86 % Following is the final summary # alignments : 31092 # unique Features these alignments represent: 30035 % of total features these alignments represent : 16.86 %