Hi there, I think I've found a bug in mismatchTable (Biostrings). It's reporting a mismatch after the end of the reported alignment. I think the code below shows the problem. thanks, as usual! Janet ##### library(Biostrings) ### couple of seqs, the middle portion aligns, but the last few bases don't. I'm not interested in those last few bases, so I do a local alignment seq1 <- DNAString("GCTGAAGTAGTTCTCCAGAA") seq2 <- DNAString("GTAGTTCTCCAAAGT") aln1 <- pairwiseAlignment ( seq1, seq2, type="local" ) aln1 # Local PairwiseAlignmentsSingleSubject (1 of 1) # pattern: [7] GTAGTTCTCCA # subject: [1] GTAGTTCTCCA # score: 21.79932 end(pattern(aln1)) # [1] 17 mismatchTable(aln1) # PatternId PatternStart PatternEnd PatternSubstring PatternQuality #1 1 18 18 G 7 # SubjectStart SubjectEnd SubjectSubstring SubjectQuality #1 12 12 A 7 #### the one mismatch that's reported is after the end of the alignment as reported above. There's another mismatch after the end of the alignment that wasn't reported sessionInfo() R Under development (unstable) (2012-10-03 r60868) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.27.2 IRanges_1.17.0 BiocGenerics_0.5.0 loaded via a namespace (and not attached): [1] parallel_2.16.0 stats4_2.16.0

Hi Janet, Thanks again for the bug report. This one should be fixed in Biostrings 2.26.2 (release) and 2.27.3 (devel). Cheers, H. On 10/10/2012 05:13 PM, Janet Young wrote: > Hi there, > > I think I've found a bug in mismatchTable (Biostrings). It's reporting a mismatch after the end of the reported alignment. I think the code below shows the problem. > > thanks, as usual! > > Janet > > ##### > > library(Biostrings) > > ### couple of seqs, the middle portion aligns, but the last few bases don't. I'm not interested in those last few bases, so I do a local alignment > seq1 <- DNAString("GCTGAAGTAGTTCTCCAGAA") > seq2 <- DNAString("GTAGTTCTCCAAAGT") > aln1 <- pairwiseAlignment ( seq1, seq2, type="local" ) > aln1 > # Local PairwiseAlignmentsSingleSubject (1 of 1) > # pattern: [7] GTAGTTCTCCA > # subject: [1] GTAGTTCTCCA > # score: 21.79932 > > end(pattern(aln1)) > # [1] 17 > > mismatchTable(aln1) > # PatternId PatternStart PatternEnd PatternSubstring PatternQuality > #1 1 18 18 G 7 > # SubjectStart SubjectEnd SubjectSubstring SubjectQuality > #1 12 12 A 7 > #### the one mismatch that's reported is after the end of the alignment as reported above. There's another mismatch after the end of the alignment that wasn't reported > > sessionInfo() > > R Under development (unstable) (2012-10-03 r60868) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.27.2 IRanges_1.17.0 BiocGenerics_0.5.0 > > loaded via a namespace (and not attached): > [1] parallel_2.16.0 stats4_2.16.0 > > _______________________________________________ > 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 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319