This reports the protocol used to align the Maize_MethylFilter_Orion features to tigrv4-genome. Fri Apr 14 18:35:21 2006 Source of Maize_MethylFilter_Orion : Methyl-filtered TIGR maize sequence, downloaded from genbank with query '(txid4577[ORGN] AND Quackenbush[AUTH] AND "methylation"[ALL] )' Alignment procedure details --------------------------- 450197 Maize_MethylFilter_Orion 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 : 191785 # unique Features these alignments represent: 173418 % of total features these alignments represent : 38.52 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 43690 150 24249 200 23050 250 20390 300 17312 350 14570 400 12185 450 9669 500 7807 550 6076 600 4538 650 3079 700 2075 750 1275 800 776 10000 1044 Alignments with matches less than 100 bp are filtered # remaining Alignments : 148589 # unique Features these remaining alignments represent: 137103 % of total features these alignments represent : 30.45 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 142713 2000 766 3000 262 4000 191 5000 231 6000 160 7000 156 8000 161 9000 97 10000 83 20000 635 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 143932 # unique Features these remaining alignments represent: 133287 % of total features these alignments represent : 29.61 % Frequency distribution of the remaining features # hits # features -------- -------- 1 127594 2 3878 3 691 4 394 5 270 6 227 8 143 9 28 10 18 20 39 30 2 40 1 50 1 100 1 Features that hit more than thrice are deleted. # remaining Alignments : 137423 # unique Features these remaining alignments represent: 132163 % of total features these alignments represent : 29.36 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 19 30 299 40 903 50 1690 60 2911 70 9256 80 15692 90 73858 100 32795 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 132013 # unique Features these remaining alignments represent: 127527 % of total features these alignments represent : 28.33 % Following is the final summary # alignments : 132013 # unique Features these alignments represent: 127527 % of total features these alignments represent : 28.33 %