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

Alan Bridge alan.bridge at isb-sib.ch
Sun Dec 2 13:29:48 EST 2007


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  

Tel: (+41 22) 379 58 90
Fax: (+41 22) 379 58 58 


More information about the Bioperl-l mailing list