PyMOL includes Biopython, so I would just use their sequence aligner. For
instance:
from Bio import pairwise2 alignments = pairwise2.align.globalxx("ACCGT", "ACG")
See http://biopython.org/DIST/docs/api/Bio.pairwise2-pysrc.html
-Spencer
On Wed, Dec 3, 2014 at 9:33 AM, Jordan Willis <[email protected]> wrote:
> Hi,
>
> I know Pymol has a built-in sequence alignment function that ‘align’ uses
> before it does alignment. I was wondering how one could access this
> function generically for any given strings. I wanted to use this in a
> module and don’t want to rely on importing alignment modules from other
> packages if I don’t have to.
>
> --
> Jordan R. Willis, Ph.D.
>
> Research Associate @Schief Lab
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> IMM Building - Room 217C
> La Jolla, CA 92037 USA
> Phone: 1-858-784-1000 ext: 43377
>
>
>
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