[Bioperl-l] number of gaps for the other sequences in an alignment

[Albert Vilella]

Hi,

It would be great if we could have a method to count, given one
sequence in an alignment, the number of gaps present in the rest of
the sequences of the alignment. That is, for each
nucleotide/aminoacidic position of the sequence of interest, look at
the column in the alignment, count the gaps, then sum them over for
the rest of the non-gapped columns in the sequence of interest.

Has anyone tried this before?

My idea is to end up having a coefficient of indel contribution for
each of the sequences in the alignment, with this coefficient being
high when one sequences forces a lot of gaps to be inserted in the
final alignment, in order to accommodate this given sequence.

I would say that the best place for this is either using methods
already available in SimpleAlign, or have something new added there.

Looking forward to your comments,

Cheers,

    Albert.