Hi Steve,

I doubt there is anything in Biostrings for this, as it is an unusual case
to score an alignment after generating the alignment, since the scoring and
the alignment are intertwined in the algorithm. I can't speak for everyone
else, but it could be a useful contribution to Biostrings.

Michael

On Tue, Apr 17, 2012 at 2:07 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> I thought I'd add to the pairwiseAlignment-related activity on the
> list today, so here's a bit of navel gazing.
>
> I *think* I want to calculate alignment scores for subsets of already
> aligned sequences and I don't think there's an easy and efficient way
> to do this without having to realign the subsets of the strings I'm
> interested in.
>
> For instance, say I have a pairwise alignment `pa`, and the result of
> `compareStrings(pattern(pa), subject(pa))` looks like something like
> this:
>
>
> "GTA?TTT?A-----TTTCATATC?TGT?TC?------------------------------------------------------CAT"
>
> Given values for the substitutionMatrix, gapOpenening, and
> gapExtension penalties used during the pairwiseAlignment, one could
> (in principle), calculate the alignment score  of the first half vs.
> the second half, or (say) running windows of length N along the
> alignment.
>
> Like I said, I *think* this is what I want to do and I was just
> curious if I'm not missing something in Biostrings that I can wire
> into ... although it's straight-forward enough to write something
> myself. In the gapOpening == gapExtension case, I can imagine
> massaging the `compareString` to an integer vector and then doing a
> simple matrix multiplication into an augmented substitutionMatrix, but
> I think the more common gapOpening != gapExtension case suggests I
> should really write a helper function in C(++).
>
> Thanks,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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