[Biopython] Is this feasible?

[Brad Chapman]

Jordan;

> Hi Brad thanks for the excellent feedback. I understand why you
> think I wouldn't need to make a new database every time but here
> is the thing. For my first hit, I want to use that sequence as a
> query in a new blast run. So it must be removed and converted into a
> fasta format to be used as the new input. So I have taken the id (
> blast_record.alignments[0].title) and I am trying to remove it from
> input.fasta. Does the fasta parser have a remove feature based on ID?
> That would be ideal.
>
> It would go something like this:
> 
> Germline
> match1
> 
> Next round:
> 
> match1
> match2
> 
> Next round:
> 
> match2:
> match3:
> 
> Where each time the hit becomes the next query.

It sounds a bit like you are re-implementing the functionality of
PSI-BLAST:

http://en.wikipedia.org/wiki/BLAST#Program

Have you given psiblast a try and found some type of issue with the
approach?

You can run and parse PSI-BLAST with Bio.Blast.Applications and the
Bio.Blast parsers:

http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc93

If you have blast+ installed, you can get all the commandline
options with:

psiblast -help

or with blast2, do:

blastpgp -

Hope this helps,
Brad