local homology search

Charlie cckim at stanford.edu
Mon Jan 21 04:53:00 EST 2002

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.


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
> ---

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net