local homology search

S.W. Rasmussen swr at crc.dk
Wed Jan 23 06:33:23 EST 2002


Dnatools will do unattended blast searches (up to 10,000 seqs per
project) against genbank databases via blastcl3 (ncbi), parse the
results into the sequence headers and allow you to list and search
the parsed data. You can download dnatools (win) at

http://www.dnatools.dk

Cheers  Soeren

--
Soeren W. Rasmussen, D.Sc., Ph.D.
Carlsberg Laboratory, Department of Physiology
10 Gl. Carlsbergvej, DK-2500, Copenhagen, Denmark
phone: +45 3327 5230 (work) +45 3616 2259 (private)
mail: swr at crc.dk

homepage: http://www.crc.dk/phys/
sequencing software: http://www.dnatools.dk
"Charlie" <cckim at stanford.edu> wrote in message
news:Pine.GSO.4.33.0201181906360.26663-100000 at elaine19.Stanford.EDU...
>
> As far as I know, you will need to download and install BLAST or FASTA and
> run it locally to do this.  I don't think any servers give permission for
> you to upload a file to run your query against (but I may be wrong).
>
> BLAST and WU-BLAST are available free for non-commercial use.  I believe
> FASTA is as well.
>
> Charlie
>
>
> On 18 Jan 2002, Lee Smith wrote:
>
> > Hi Guys
> >
> > This is what I want to do:
> > I have a large sequence, from which I have identified all ORFs of
> > greater than 30aa in length (there are approx 1000 of these). I want
> > to place these ORFs into a file, and then search for homology to
> > various protein 'query' sequences.
> >
> > Can FASTA or  BLAST be used to search local files (I know you can
> > search a file of filenames)?
> > If not, does anyone have any other suggestions?
> >
> >
> > Cheers
> >
> > Lee
> > --
> >
> >
> > Dr Lee Smith
> > UWA Dept of Microbiology
> > QEII Medical Centre
> > Nedlands
> > WA 6009
> > Australia
> >
> > LMSmith at cyllene.uwa.edu.au
> >
> > 08 9346 3587
> >
> > ---
> >
> >
>






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