[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

Avril Coghlan
University College Cork
Ireland



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