This reports the protocol used to align the Maize_HiCotCluster_TIGR features to tigrv4-genome. Fri Apr 14 18:25:04 2006 Source of Maize_HiCotCluster_TIGR : from Gramene markers database, originally Downloaded from TIGR using the link ftp://ftp.tigr.org/pub/data/MAIZE/AZMs/release_4.0/zmg_fasta.4.0HC_022304.gz Alignment procedure details --------------------------- 172600 Maize_HiCotCluster_TIGR 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 : 61368 # unique Features these alignments represent: 54399 % of total features these alignments represent : 31.52 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 19600 150 8601 200 7028 250 5406 300 4036 350 3312 400 2623 450 2086 500 1697 550 1308 600 1046 650 835 700 683 750 574 800 565 10000 1968 Alignments with matches less than 100 bp are filtered # remaining Alignments : 41986 # unique Features these remaining alignments represent: 38056 % of total features these alignments represent : 22.05 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 38840 2000 1525 3000 291 4000 106 5000 75 6000 45 7000 45 8000 33 9000 30 10000 26 20000 168 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 40762 # unique Features these remaining alignments represent: 36974 % of total features these alignments represent : 21.42 % Frequency distribution of the remaining features # hits # features -------- -------- 1 35108 2 1180 3 217 4 169 5 142 6 68 8 42 9 12 10 17 20 18 30 0 40 1 50 0 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 38119 # unique Features these remaining alignments represent: 36505 % of total features these alignments represent : 21.15 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 3 30 65 40 275 50 651 60 1138 70 2203 80 5248 90 21994 100 6542 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 36112 # unique Features these remaining alignments represent: 34685 % of total features these alignments represent : 20.10 % Following is the final summary # alignments : 36112 # unique Features these alignments represent: 34685 % of total features these alignments represent : 20.10 %