[BioPython] help for local alignment

[Peter]

On Mon, Dec 22, 2008 at 4:38 PM, Chandan Kumar <biopython.chen at gmail.com> wrote:
> Dear all,
>                 can any one provide me simple code for local alignment
> python code which can be applied for protein or nucleotide sequence. Please
> provide me the simplest code as I am new to python and from biology
> background.
>
> Thanking you.
>
> Kind regards
> Chen

Hi Chen,

Are you wanting to do pairwise alignments (aligning two sequences to
each other), or multiple sequence alignments?

For multiple sequence alignments, you might want to use a 3rd party
tool like ClustalW, or MUSCLE. Biopython can parse several alignment
formats including ClustalW format.  See our tutorial for examples
using ClustalW.

Biopython's Bio.pairwise2 can do pairwise alignments, although we only
have the built in documentation for this at the moment (nothing in our
tutorial).  This documentation is also available online:
http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html

For pairwise sequence alignments I personally use the EMBOSS tools
"water" (Smith-Waterman algorithm for local alignment) or "needle"
(Needleman-Wunsch for global alignment).  Biopython's Bio.AlignIO
module can parse their output.

Peter