This reports the protocol used to align the Ryegrass_MethylFilterCluster_Orion features to tigrv4-genome. Mon Apr 24 16:39:36 2006 Source of Ryegrass_MethylFilterCluster_Orion : from Gramene markers database, originally Obtained from Orion Genomics Alignment procedure details --------------------------- 80162 Ryegrass_MethylFilterCluster_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 : 24206 # unique Features these alignments represent: 22490 % of total features these alignments represent : 28.06 % The length of the matches are distributed as follows Hit_length # alignments -------- -------- 100 5750 150 3063 200 2873 250 2532 300 2063 350 1636 400 1347 450 1143 500 858 550 664 600 535 650 397 700 302 750 225 800 179 10000 639 Alignments with matches less than 100 bp are filtered # remaining Alignments : 18534 # unique Features these remaining alignments represent: 17663 % of total features these alignments represent : 22.03 % gap distribution of the remaining features gaps # alignments -------- -------- 1000 17207 2000 346 3000 66 4000 48 5000 29 6000 26 7000 40 8000 20 9000 33 10000 23 20000 166 Alignments with gaps > 4000 bp are filtered # remaining Alignments : 17667 # unique Features these remaining alignments represent: 16898 % of total features these alignments represent : 21.08 % Frequency distribution of the remaining features # hits # features -------- -------- 1 16436 2 337 3 70 4 20 5 17 6 7 8 8 9 0 10 1 20 1 30 0 40 0 50 0 100 1 Features that hit more than thrice are deleted. # remaining Alignments : 17320 # unique Features these remaining alignments represent: 16843 % of total features these alignments represent : 21.01 % % Identity distribution of the remaining features % Identity # alignemnts -------- -------- 10 0 20 2 30 27 40 98 50 205 60 323 70 587 80 1952 90 9933 100 4193 Alignments with percent identity lower than 60 deleted. # remaining Alignments : 16707 # unique Features these remaining alignments represent: 16289 % of total features these alignments represent : 20.32 % Following is the final summary # alignments : 16707 # unique Features these alignments represent: 16289 % of total features these alignments represent : 20.32 %