cjfields at uiuc.edu
Mon Dec 3 09:04:06 EST 2007
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
A list of current databases can be found here:
On Dec 2, 2007, at 12:29 PM, Alan Bridge wrote:
> 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
> 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
> Tel: (+41 22) 379 58 90
> Fax: (+41 22) 379 58 58
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