This reports the protocol used to align the Ryegrass_MethylFilter_Orion features to tigrv4-genome. Fri Apr 14 18:13:28 2006 Source of Ryegrass_MethylFilter_Orion : from Gramene markers database, originally Obtained from Orion Genomics Alignment procedure details --------------------------- 398333 Ryegrass_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 : 81248 # unique Features these alignments represent: 66901 % of total features these alignments represent : 16.80 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 22533 150 11739 200 10216 250 8512 300 6656 350 5176 400 3956 450 2993 500 2265 550 1742 600 1583 650 1357 700 902 750 809 800 612 10000 197 Alignments with matches less than 100 bp are filtered # remaining Alignments : 58992 # unique Features these remaining alignments represent: 48489 % of total features these alignments represent : 12.17 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 56854 2000 125 3000 65 4000 71 5000 78 6000 63 7000 62 8000 39 9000 60 10000 46 20000 329 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 57115 # unique Features these remaining alignments represent: 46945 % of total features these alignments represent : 11.79 % Frequency distribution of the remaining features # hits # features -------- -------- 1 43730 2 1382 3 289 4 309 5 328 6 403 8 402 9 44 10 18 20 24 30 7 40 3 50 2 100 4 Features that hit more than thrice are deleted. # remaining Alignments : 47361 # unique Features these remaining alignments represent: 45401 % of total features these alignments represent : 11.40 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 7 30 117 40 267 50 571 60 1728 70 2489 80 5435 90 25227 100 11520 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 44880 # unique Features these remaining alignments represent: 43264 % of total features these alignments represent : 10.86 % Following is the final summary # alignments : 44880 # unique Features these alignments represent: 43264 % of total features these alignments represent : 10.86 %