[Biopython] Blast Two Sequences

[Islam Amin]

Thank you all for you comments, The idea behind my work is, that I'm trying
to used blast to align many pairs of sequences by using blast NCBI not
EMBOSS or Pairwise2, therefore I need to pass these sequences on the fly
instead of writing fasta file in H.D.

On Sat, Mar 11, 2017 at 5:05 AM, Jan T Kim <jttkim at googlemail.com> wrote:

> Hi All,
>
> after a quick look at this matter I'm rather puzzled by what the purpose
> of all this is. Do you want to align the first sequence to the second
> sequence? Then, doing that via NCBI BLAST is a really weird way of
> achieving this, my suggestions would be to (1) consider using a pairwise
> alignment program and (2) run the alignment locally on your computer --
> e.g. install EMBOSS, then you can use BioPython's EMBOSS command line
> adapters.
>
> Or do you want to scan some NCBI database (non-redundant nucleotide or
> protein, typically) using both sequences? That's not what that script does,
> as far as I can tell, though.
>
> Best regards, Jan
>
>
> On Fri, Mar 10, 2017 at 05:15:33PM +0000, Peter Cock wrote:
> > Good idea Lenna, but that only works within Python. Here we need to
> provide
> > the FASTA format sequence data to NCBI BLAST.
> >
> > If there was only one input file involved, Islam might be able to pipe
> that to
> > BLAST using stdin. However, there there are two input files so I don't
> see
> > any easy way to do this other than two temporary files.
> >
> > Peter
> >
> > On Thu, Mar 9, 2017 at 11:38 PM, Lenna Peterson
> > <lenna.peterson at gmail.com> wrote:
> > > Hi Islam,
> > >
> > > If you need to avoid writing the sequence to disk for whatever reason,
> you
> > > could create an in-memory file using StringIO:
> > > https://docs.python.org/2/library/stringio.html
> > >
> > > Lenna
> > _______________________________________________
> > Biopython mailing list  -  Biopython at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/biopython
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>



-- 
Best Regards,
Islam Amin.

www.egyptscience.net
Scientific Research Group in EGYPT
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170311/ead7d22f/attachment-0003.html>