Hi there, I've been trying to figure out whether I can use some of your very nice alignment utilities (e.g. mismatchTable) on pairwise alignments I've generated in other ways than pairwiseAlignment? For example, alignments I've generated using programs outside of R, and then read in using readDNAMultipleAlignment or readDNAStringSet. I've been poking around a bit and can't see a way to do it, but I might be missing something - maybe there's some kind of coercion I should do? If there isn't a way to run mismatchTable on outside alignments, can I put in a plug for it - it'd be really useful for me, at least. thanks very much, Janet ------------------------------------------------------------------- Dr. Janet Young Tapscott and Malik labs Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA. tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung ...at... fhcrc.org -------------------------------------------------------------------

Hi Janet, I don't think there is anything like that, but I have looked for it and wanted it on occasion. Always found a workaround, though. I guess there could be a constructor that would take a DNAStringSet for the pattern and a DNAString/Set for the subject and assume that the gaps have already been inserted. It would then calculate the mismatch information. Michael On Tue, Oct 9, 2012 at 6:49 PM, Janet Young <jayoung@fhcrc.org> wrote: > Hi there, > > I've been trying to figure out whether I can use some of your very nice > alignment utilities (e.g. mismatchTable) on pairwise alignments I've > generated in other ways than pairwiseAlignment? For example, alignments > I've generated using programs outside of R, and then read in using > readDNAMultipleAlignment or readDNAStringSet. > > I've been poking around a bit and can't see a way to do it, but I might be > missing something - maybe there's some kind of coercion I should do? > > If there isn't a way to run mismatchTable on outside alignments, can I put > in a plug for it - it'd be really useful for me, at least. > > thanks very much, > > Janet > > ------------------------------------------------------------------- > > Dr. Janet Young > > Tapscott and Malik labs > > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., C3-168, > P.O. Box 19024, Seattle, WA 98109-1024, USA. > > tel: (206) 667 1471 fax: (206) 667 6524 > email: jayoung ...at... fhcrc.org > > > ------------------------------------------------------------------- > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]