[BioC] feature request - pairwiseAlignment() in Biostrings

Coghlan, Avril A.Coghlan at ucc.ie
Thu Jul 22 10:54:11 CEST 2010

Dear Patrick and Steve,

I am wondering whether it would be possible to add an option to the
pairwiseAlignment() function in Biostrings, so that it could print out:
(i) all the top-scoring alignments for 2 sequences, if there are more
than one equally scoring top-scoring alignments ?
(ii) the top X top-scoring alignments for 2 sequences, where the user
specifies the number X, and where the X alignments don't have to have
equal scores, but are ordered by decreasing score ?

I'm not sure if these options are easy to add, but would be very useful
if you could add them.

If you haven't time to do this, I would be willing to try to help add
the features to the pairwiseAlignment() function, if you can point me
towards the code.

Kind Regards,

Avril Coghlan
University College Cork

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