This reports the protocol used to align the Maize_HiCotMethylFilterCluster_TIGR features to tigrv4-genome. Fri Apr 14 18:18:46 2006 Source of Maize_HiCotMethylFilterCluster_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.4.0ALL_022304.gz Alignment procedure details --------------------------- 243807 Maize_HiCotMethylFilterCluster_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 : 102676 # unique Features these alignments represent: 86409 % of total features these alignments represent : 35.44 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 31740 150 11003 200 9278 250 7543 300 6329 350 5352 400 4680 450 4134 500 3609 550 2909 600 2500 650 2039 700 1710 750 1502 800 1461 10000 6887 Alignments with matches less than 100 bp are filtered # remaining Alignments : 71229 # unique Features these remaining alignments represent: 61442 % of total features these alignments represent : 25.20 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 62023 2000 3445 3000 1111 4000 569 5000 295 6000 144 7000 124 8000 117 9000 82 10000 55 20000 461 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 67148 # unique Features these remaining alignments represent: 58030 % of total features these alignments represent : 23.80 % Frequency distribution of the remaining features # hits # features -------- -------- 1 53650 2 2699 3 593 4 379 5 293 6 199 8 120 9 22 10 30 20 39 30 1 40 2 50 2 100 1 Features that hit more than thrice are deleted. # remaining Alignments : 60827 # unique Features these remaining alignments represent: 56942 % of total features these alignments represent : 23.36 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 16 30 277 40 925 50 1767 60 2850 70 7573 80 8364 90 29605 100 9450 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 55360 # unique Features these remaining alignments represent: 52151 % of total features these alignments represent : 21.39 % Following is the final summary # alignments : 55360 # unique Features these alignments represent: 52151 % of total features these alignments represent : 21.39 %