This reports the protocol used to align the Maize_MethylFilter_CSHL features to tigrv4-genome. Fri Apr 14 12:09:00 2006 Source of Maize_MethylFilter_CSHL : Methyl-filtered CSHL maize sequence, downloaded from genbank with query '(txid4577[ORGN] AND McCombie[AUTH] AND methyl[TITL] AND 2002[MDAT])' Alignment procedure details --------------------------- 66390 Maize_MethylFilter_CSHL 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 : 37990 # unique Features these alignments represent: 21014 % of total features these alignments represent : 31.65 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 7239 150 3527 200 3276 250 2664 300 2134 350 2050 400 1970 450 1878 500 1883 550 2262 600 2563 650 2536 700 2346 750 1194 800 405 10000 63 Alignments with matches less than 100 bp are filtered # remaining Alignments : 30810 # unique Features these remaining alignments represent: 15576 % of total features these alignments represent : 23.46 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 30355 2000 27 3000 9 4000 27 5000 21 6000 7 7000 3 8000 17 9000 2 10000 13 20000 30 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 30418 # unique Features these remaining alignments represent: 15245 % of total features these alignments represent : 22.96 % Frequency distribution of the remaining features # hits # features -------- -------- 1 11133 2 1071 3 736 4 625 5 507 6 232 8 453 9 125 10 177 20 184 30 1 40 0 50 0 100 1 Features that hit more than thrice are deleted. # remaining Alignments : 15483 # unique Features these remaining alignments represent: 12940 % of total features these alignments represent : 19.49 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 1 30 20 40 68 50 121 60 336 70 1072 80 1441 90 5685 100 6739 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 14991 # unique Features these remaining alignments represent: 12506 % of total features these alignments represent : 18.84 % Following is the final summary # alignments : 14991 # unique Features these alignments represent: 12506 % of total features these alignments represent : 18.84 %