# HG changeset patch # User xuebing # Date 1331926029 14400 # Node ID e0813fcccd4188d09a6fba286fc48d206a285ce9 # Parent 8cec2078632a1c83ee3ca1702e5c622851342d29 Deleted selected files diff -r 8cec2078632a -r e0813fcccd41 match Binary file match has changed diff -r 8cec2078632a -r e0813fcccd41 match.xml --- a/match.xml Fri Mar 16 14:15:10 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ - - find short motif occurrences - ./match $motif $seq $output $nmismatch $rc $bed > $log - - - - - - - - - - - - - - -**What it does** - -This tool searches occurrences of a short nucleotide seuqences (allowing mismatches) in a set of longer sequences. - -Example motif file:: - - >motif1 - CAGGTAAGT - >motif2 - GTTTGGGGGCC - -Example sequence file:: - - >hg18_chr6_122208322_122209078_+ - CGTCGTAGCTACTAGCTACGTACGTACGTAGCTAGCATGCATGCTACGTA - CGTAGCTAGCTAAAAAAAAAAAAAAACTGCGGCTAGCTAGCTAGCTACGT - CGATCGTAGCTAC... - >hg18_chr6_1208322_122209023_+ - CGATGCTAGCTAGCTAGCTACGTAGCTAGCTAGTCGATGCTAGCTAGCTA - ATGCTAGCTAGC.... - -Output (bed):: - - chr11 72790893 72790902 ACTTAACTG 1 - antisense 5ss,G4T:CAGTTAAGT-rc hg18_chr11_72790846_72791902_+ 47 - chr11 72791880 72791889 CAGGTAAGA 1 + sense 5ss,T9A:CAGGTAAGA hg18_chr11_72790846_72791902_+ 1034 - - -Output (tab):: - - Tmod4 802 5ss:CAGGTAAGT-rc ACTTACCTG - Atp7b 77 5ss:CAGGTAAGT CAGGTAAGT - Fnta 665 5ss:CAGGTAAGT CAGGTAAGT - - - - -