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
>
>
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>
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