i found a wired problem, but i donot know if it is a bug triming from left is different from triming from right, please see those coding such two sequence have distance of 3 AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCA TCACATCACGATATCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG subject<- DNAString("AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCATCAC ATCACGATATCGTATGCCGTCTTCTGCTTG") PCR2rc <- DNAString("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCT GCTTG") trimLRPatterns(Rpattern = PCR2rc, subject = subject, max.Rmismatch=0.2,with.Rindels=T) or trimLRPatterns(Rpattern = PCR2rc, subject = subject, max.Rmismatch=3,with.Rindels=T) 25-letter "DNAString" instance seq: AAAAAAAAAAAAAAACGACACAAGC such two sequence are symitric of those above GATCGGAAGAGCACACGTCTGAACTCCA TCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG subject<- DNAString("GATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGC TTGAAAAAAAAAAAAAAACGACACAAGCCC") PCR2rc <- DNAString("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCT GCTTG") trimLRPatterns(Lpattern = PCR2rc, subject = subject, max.Lmismatch=0.2,with.Rindels=T) 88-letter "DNAString" instance seq: ATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAA AAAAAACGACACAAGCCC [[alternative HTML version deleted]]

The supposed counter-example (see below) suffers the same inherent defect as in your last query: using 'with.*R*indels=T' with an 'Lpattern'. Fixing that defect defeats the counter-example, unless I've missed something. On Oct 11, 2011, at 11:55 AM, wang peter wrote: > i found a wired problem, but i donot know if it is a bug > > triming from left is different from triming from right, please see > those > coding > > such two sequence have distance of 3 > AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCA > TCACATCACGATATCGTATGCCGTCTTCTGCTTG > > AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG > > subject<- > DNAString > ("AAAAAAAAAAAAAAACGACACAAGCCCGATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATA > TCGTATGCCGTCTTCTGCTTG") > PCR2rc <- > DNAString > ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG") > trimLRPatterns(Rpattern = PCR2rc, subject = subject, > max.Rmismatch=0.2,with.Rindels=T) > or trimLRPatterns(Rpattern = PCR2rc, subject = subject, > max.Rmismatch=3,with.Rindels=T) > 25-letter "DNAString" instance > seq: AAAAAAAAAAAAAAACGACACAAGC > > such two sequence are symitric of those above > > GATCGGAAGAGCACACGTCTGAACTCCA > TCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACGACACAAGCCC > AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG > > subject<- > DNAString > ("GATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAA > AAAAAAAAACGACACAAGCCC") > PCR2rc <- > DNAString > ("AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG") > trimLRPatterns(Lpattern = PCR2rc, subject = subject, > max.Lmismatch=0.2,with.Rindels=T) > > 88-letter "DNAString" instance > seq: > ATCGGAAGAGCACACGTCTGAACTCCATCACATCACGATATCGTATGCCGTCTTCTGCTTGAAAAAAAAA > AAAAAACGACACAAGCCC But, > trimLRPatterns(Lpattern = PCR2rc, subject = subject, max.Lmismatch=0.2, with.Lindels=T) 25-letter "DNAString" instance seq: AAAAAAAAAAAAACGACACAAGCCC > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor