[Bioperl-l] Bio::Tools::Run::RemoteBlast

[Chris Fields]

You are limited to the databases hosted on the NCBI server, so it's  
really up to them; RemoteBlast is an interface to NCBI's WebBlast  
using URLAPI.

A list of current databases can be found here:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html

chris

On Dec 2, 2007, at 12:29 PM, Alan Bridge wrote:

> Hello,
>
> I was just wondering if, when performing a RemoteBlast, it would be
> possible to specify the entire UniProt database (i.e. Swiss-Prot +
> TrEMBL), or even just TrEMBL.
>
> It seems that currently, you can only specify Swiss-Prot (the  
> annotated
> portion of UniProt, which is much smaller than its automatically
> annotated counterpart, TrEMBL). Any hints on how to expand the search
> space to include TrEMBL would be really appreciated.
>
> Regards, Alan Bridge
>
>            my $prog = 'blastp';
>            my $db   = 'swissprot'; # use TrEMBL ?
>            my $e_val= '1e-10';
>
>            my @params = ( '-prog' => $prog, '-data' => $db, '-expect'
> => $e_val, '-readmethod' => 'SearchIO' );
>
> -- 
> Alan Bridge PhD
> Swiss-Prot annotator
> Swiss Institute of Bioinformatics (SIB)
> 1, rue Michel Servet
> CH-1211 Geneva 4
> Switzerland
>
> Tel: (+41 22) 379 58 90
> Fax: (+41 22) 379 58 58
>
> http://www.expasy.org/