[Biopython] matching sequences from fasta files

[Vincent Davis]

@Michiel de Hoon
Nexalign can do exactly what you are trying to do.
See http://genome.gsc.riken.jp/osc/english/dataresource/.

Thanks for the link to nextalign. It is perfect and fast. This is exactly
what I needed. I already have the results I needed 5min from download to
results. Need to spend a little time verifying I have what I what but it
looks right.
Again thank you very much.
*
*

*Vincent Davis
720-301-3003 *
vincent at vincentdavis.net
 my blog <http://vincentdavis.net> |
LinkedIn<http://www.linkedin.com/in/vincentdavis>


On Thu, Mar 11, 2010 at 5:36 PM, Michiel de Hoon <mjldehoon at yahoo.com>wrote:

> --- On Thu, 3/11/10, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> > From: Peter <biopython at maubp.freeserve.co.uk>
> > Subject: Re: [Biopython] matching sequences from fasta files
> > To: "Vincent Davis" <vincent at vincentdavis.net>
> > Cc: "biopython" <biopython at lists.open-bio.org>
> > Date: Thursday, March 11, 2010, 6:06 AM
> > On Thu, Mar 11, 2010 at 12:47 AM,
> > Vincent Davis
> > <vincent at vincentdavis.net>
> > wrote:
> > > So I had an idea and wanted to get some feedback.
> > > I could make all possible single position mismatches
> > for the sequences. I
> > > have 230,000 now and the would give me 17,250,000 (3 *
> > 25 * 230,000). Then
> > > use BLAST to look for perfect matches. I would
> > probably do this
> > > incrementally maybe even just blast for each sequence.
> > The advantage I see
> > > in this is that BLAST can run multi core and I am
> > running it on an 8core
> > > with 48gb of memory So it seems that this would be the
> > fastest way to do
> > > this and very straight forward as there is very little
> > parsing. There is
> > > either a match or not. I am purely guessing that
> > generating the list if
> > > faster than parsing the results.
> >
> Nexalign can do exactly what you are trying to do.
> See http://genome.gsc.riken.jp/osc/english/dataresource/.
>
> --Michiel.
>
>
>
>