This reports the protocol used to align the Rice_FSTtransposon features to tigrv4-genome. Fri Apr 14 11:52:22 2006 Source of Rice_FSTtransposon : UCD FSTs from Gramene markers database, originally downloaded from genebank using "transposon AND insertion lines AND oryza[Organism]" Alignment procedure details --------------------------- 4183 Rice_FSTtransposon are aligned to tigrv4-genome using blat with blat parameters -minScore=160 followed by PslReps with -minAli=0.90 -nearTop=0.01 -singleHit. This was followed by a filtering procedure described below and applied in general to 'Same Species Genomic' data sets. Initial summary # alignments : 4162 # unique Features these alignments represent: 3476 % of total features these alignments represent : 83.10 % Following is the GAP distribution Gaps # alignments -------- -------- 0 2654 1 388 2 144 3 96 4 61 5 62 6 39 7 45 8 22 9 30 10 29 20 154 30 138 40 53 50 37 60 54 70 19 80 10 90 5 100 13 200 40 300 14 400 14 500 13 600 0 700 0 800 1 900 0 10000 0 Features with gaps > 40 bp are deleted # remaining Alignments : 3915 # unique Features these remaining alignments represent: 3294 % of total features these alignments represent : 78.75 % Following is the distribution of by feature coverage %coverage # alignments -------- -------- 9 0 19 0 29 5 39 13 49 71 59 168 69 212 79 329 89 518 90 89 91 90 92 97 93 128 94 103 95 130 96 146 97 204 98 182 99 266 100 1164 Features less than 90 % coverage are deleted. # remaining Alignments : 2513 # unique Features these remaining alignments represent: 2251 % of total features these alignments represent : 53.81 % % Identity distribution of the remaining features % Identity # alignments -------- -------- 90 3 91 8 92 3 93 7 94 14 95 31 96 63 97 88 98 229 99 721 100 1346 Features less than 92 % identity are deleted. # remaining Alignments : 2502 # unique Features these remaining alignments represent: 2240 % of total features these alignments represent : 53.55 % Frequency distribution of the remaining features # hits # features -------- -------- 1 2186 2 20 3 4 4 0 5 2 6 1 8 26 9 0 10 0 20 0 30 0 40 0 50 1 100 0 Features that hit more than thrice are deleted. # remaining Alignments : 2238 # unique Features these remaining alignments represent: 2210 % of total features these alignments represent : 52.83 %