[Bioperl-l] re: blast database()

[Steve Chervitz]

The Bio::Tools::Blast::Sbjct::database() method no longer provides any useful
information. It's been unofficially deprecated for some time. The reason is that
extracting database info from the sequence identifier in a BLAST hit was highly
error-prone, so this is no longer done. The Bio::Tools::Blast::database() probably
gets you what you need. Or, better, switch over to the new Bio::SearchIO facility as
Jason mentioned. The Result object has a database_name() method. (Again, note that
there is no hit-specific database method in the new SearchIO system).

Steve 
--
Steve Chervitz 
sac@bioperl.org

--- Seth Redmond <seth.redmond@ic.ac.uk> wrote:
> I'm having some trouble getting the blast::hits... database() method to 
> work. (i.e. to find the exact fasta sequence I'm matching against in my 
> database.
> 
> $database = @hits[$j]->database();
> 
> returns a dash instead of the database name. I've tried a number of 
> different databases with this. Are there any relevant examples which I 
> might have a look at? Anyone have any advice?
> 
> thanks
> 
> -s
> 
> --
> ______________________________________________
> Seth Redmond
> 
> DNA resource and Database Curator
> Wellcome Trust Laboratories for Molecular Parasitology
> Department of Biological Sciences
> Imperial College
> London
> SW7 2AY
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