[Bioperl-l] recovering blast query_name
Wed, 20 Nov 2002 15:34:18 -0600
I think the critical thing is that the header line for the sequence is formatted in a way that blast likes it. To test whatever you want, go to the NCBI blast page, and cut and paste your sequence there. If you get a query name back, then that is what remote blast will give you. SO a blast without the header gives no query name? For example, this
>gi|21389487|ref|NP_653312.1| hypothetical protein MGC22679 [Homo sapiens]
results in a query name of gi|21389487|ref|NP_653312.1|
Does that help? Try it and let me know...
> -----Original Message-----
> From: Lewis Lukens [mailto:email@example.com]
> Sent: Wednesday, November 20, 2002 2:49 PM
> To: firstname.lastname@example.org
> Subject: [Bioperl-l] recovering blast query_name
> Sorry for a basic question... I have been trying to use the
> Bio::Tools:Run:RemoteBlast module to blast a single file with many
> fasta formated sequences against ncbi nt and parse the blast reports.
> Almost everything is working well. I get all the hit and hsp
> features for all the hits. I can recover the query sequence, but I
> can't seem to recover the query sequence names. How does one do this?
> I used almost the exact code as in the Remoteblast Synopsis
in this code, this expression works:
print "db is ", $result->database_name(), "\n";
but, these expressions return empty fields:
my $name = $result->query_name();
my $desc = $result->query_description();
my $acc= $result->query_accession();
I have been using SearchIO to parse blast output files and never had
this problem before. Any ideas?
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