[Bioperl-l] recovering blast query_name

Wiepert, Mathieu Wiepert.Mathieu@mayo.edu
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:llukens@uoguelph.ca]
> Sent: Wednesday, November 20, 2002 2:49 PM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] recovering blast query_name
> Hello,
> 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
> http://doc.bioperl.org/releases/bioperl-1.0.2/Bio/Tools/Run/Re

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?

Thanks much,
Lewis Lukens
Assistant Professor
Department of Plant Agriculture
Univ. of Guelph, Guelph, Ontario. N1G 2W1

Tel: (519) 824- 4120 ext 2304
Bioperl-l mailing list