[Bioperl-l] Remote Blast question.

[Will Fischer]

<pathetic request from naive user>

I need help for remote blasts.

NCBI's interface changes have disabled the example scripts distributed
with bioperl-0.7.0 and earlier, which had met my needs so that I didn't
have to figure out OO perl and bioperl.

Needing to perform some remote blasts, I installed RemoteBlast.pm --
but I am, alas, a mere mortal, and <simply> want to blast my stuff.
Can some kind soul supply me with an equivalent to run_remote_blast.pl,
whereby I could just get done what I need to do? (remotely blastx my new
sequences to ID those clones I need to sequence the other strand of and
those I can just throw away).

</pathetic request from naive user>

Sure, it would be better for me to actually figure it out myself -- but
first I have to finish my thesis.  Thanks for your help.


-- Will Fischer

Jason Stajich <jason@chg.mc.duke.edu> wrote:

We have a module that will do this - see Bio::Tools::Run::RemoteBlast.

Bio::Tools::Blast will not contain remote blast code in the future and
may not exist in future bioperl releases.  We have split this
functionality into a separate module.  ...

On Mon, 28 May 2001, Mark Hoebeke wrote:

> 
> needing to perform some remote Blasts, I looked at the Bio::Tools::Blast
> documentation (and, the run_blast_remote.pl and retrieve_blast.pl example
> scripts). It seems, the remote execution module is unable to retrieve any
> Blast result, or even, achieve correct remote execution of the Blast
> query. ...
> 
> Does this mean that managing remote execution is doomed due to too
> frequent changes in the Blast query format ? ...