[Bioperl-l] Bio::SimpleAlign methods

[Richard Adams]

Hello,
    I'm writing a wrapper for the SIFT program which predicts functional
effects of SNPs using protein sequence
alignments and have written 3 methods for formatting alignments
necessary for input into this program and maybe useful for others as
well.

    1. $aln->get_ungapped_slices($seq_id);
        returns an array of alignment slices corresponding to ungapped
sequence blocks of the specified  sequence.

    2. $aln->merge_slices();
        concatenates alignment slices into 1 big alignment.

    3. $aln->set_pos($seq_id, pos);
        changes the position of a sequence in the alignment

    If these are of any potential use should I CVS them into
Bio::SimpleAlign (or given they're rather esoteric) into
Bio::Align::Utilities?

Richard

--
Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk