[Biopython] clustalw align multiple sequences to reference.

[Eric Talevich]

On Wed, Jul 13, 2011 at 2:40 PM, Daniel Jones <lawson.jones at gmail.com>wrote:

> Hi Biopython users,
> I have a file with many (~50,000) 200 bp sequences, each of which I would
> like to align to a fixed reference sequence. I *don't* care about aligning
> all 50,000 sequences with each other; I only care about aligning each one
> with the reference sequence. I can't figure out a way to do this without
> generating 50,000 files, which seems like ridiculous unnecessary overhead.
> It seems like ClustalW's interface is quite inflexible in demanding
> separate
> input and output files for each alignment, but I don't have much experience
> using it so maybe I'm completely missing something.
>
> Incidentally, I'm not wedded to the idea of using ClustalW, so if there's
> an
> alternate alignment program that would make this easier, I'd certainly be
> open to trying it.
>
>
Are these reads from sequencing? If so, then BWA or Bowtie might be what you
want:

http://bio-bwa.sourceforge.net/
http://bowtie-bio.sourceforge.net/index.shtml

If not, then you could try BLAST with your reference sequence as the query
and the short sequences as your database.

Cheers,
Eric