[Bioperl-l] recovering blast query_name

[Wiepert, Mathieu]

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]
MKILLVFDFDNTIIDDNSDTWIVQCAPNKKLPIELRDSYRKGFWTEFMGRVFKYLGDKGVREHEMKRAVT
SLPFTPGMVELFNFIRKNKDKFDCIIISDSNSVFIDWVLEAASFHDIFDKVFTNPAAFNSNGHLTVENYH
THSCNRCPKNLCKKVVLIEFVDKQLQQGVNYTQIVYIGDGGNDVCPVTFLKNDDVAMPRKGYTLQKTLSR
MSQNLEPMEYSVVVWSSGVDIISHLQFLIKD

results in a query name of gi|21389487|ref|NP_653312.1|

Does that help?  Try it and let me know...

-Mat

> -----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
moteBlast.html

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

Tel: (519) 824- 4120 ext 2304
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