This reports the protocol used to align the RiceJaponica_cDNA_KOME features to tigrv4-genome. Fri Apr 14 14:46:29 2006 Source of RiceJaponica_cDNA_KOME : from Gramene markers database, originally Downloaded from Genbank with query 'FLI_CDNA[Keyword] AND Oryza[Organism] AND Kikuchi[Author]' Alignment procedure details --------------------------- 32127 RiceJaponica_cDNA_KOME are aligned to tigrv4-genome using blat with blat parameters -minScore=120 followed by PslReps with -singleHit. This was followed by a filtering procedure described below and applied in general to 'Coding-SameSpecies' data sets. Initial summary # alignments : 31511 # unique Features these alignments represent: 30670 % of total features these alignments represent : 95.46 % The following is the distribution of the feature coverage %coverage no of alignments -------- -------- 9 16 19 63 29 31 39 58 49 47 59 233 69 205 79 174 89 219 90 24 91 16 92 30 93 30 94 27 95 31 96 44 97 66 98 102 99 270 100 29825 Alignments less than 95 % coverage are deleted # remaining Alignments : 30307 # unique Features these remaining alignments represent: 29869 % of total features these alignments represent : 92.97 % GAP distribution of the remaining features Gaps # alignments -------- -------- 1000 14106 2000 6472 3000 4509 4000 2318 5000 1105 6000 635 7000 366 8000 241 9000 174 10000 102 20000 231 Alignments with gaps > 4000 bp are deleted # remaining Alignments : 27405 # unique Features these remaining alignments represent: 26989 % of total features these alignments represent : 84.01 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 0 91 0 92 0 93 0 94 0 95 0 96 1 97 5 98 9 99 12984 100 14406 Frequency distribution of the remaining features # hits # features -------- -------- 1 26806 2 105 3 27 4 14 5 11 6 17 8 5 9 1 10 1 20 1 30 1 40 0 50 0 100 0 Features that hit more than four times are deleted. # remaining Alignments : 27153 # unique Features these remaining alignments represent: 26952 % of total features these alignments represent : 83.89 %