[Biopython] Blast Two sequences from a python script

[Peter Cock]

On Sun, Apr 15, 2012 at 8:55 AM, Laura Scearce <flitrfli at gmail.com> wrote:
> I have a list of pairs of proteins and I want to compare speed and accuracy
> of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know
> there is a "Blast Two Sequences" option on NCBI website, but I would like
> to run it from a python script. Perhaps Biopython has this capability? If I
> cannot use Blast Two Sequences, I will compare different versions of
> Smith-Waterman, but this would not be nearly as exciting :) OR, if anyone
> has another idea for a great senior year project in Bioinformatics
> involving comparing pairs of proteins, please don't hesitate to let me
> know！ Thank you in advance.

I would suggest looking at the EMBOSS tool water for Smith-Waterman
alignments. http://emboss.open-bio.org/wiki/Appdoc:Water

See also: http://emboss.open-bio.org/wiki/Appdoc:Needle
and http://emboss.open-bio.org/wiki/Appdoc:Matcher

For BLAST, the simplest option might be to generate temporary
input FASTA files, then use the BLAST+ command line tools with
the -query and -subject options. This way you don't have to make
temporary BLAST databases (although it isn't quite as fast).

Peter