[Bioperl-l] help on blastcl3

[Chris Fields]

This isn't relevant to bioperl.   Try NCBI's BLAST help email:

blast-help at ncbi.nlm.nih.gov
   
Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sanjib Kumar Gupta
> Sent: Friday, March 10, 2006 2:16 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] help on blastcl3
> 
> 
> Hi
> 
> I am very new using blastcl3.
> When I use
> ./blastcl3 -p blastn -d nr -i nuc -o out.blast
> 
> I getting the following result in out.blast
> 
> BLASTN 2.2.13 [Nov-27-2005]
> 
> 
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database search
> programs",  Nucleic Acids Res. 25:3389-3402.
> 
> Query= gi|145773|gb|K01298.1|ECODNAK Escherichia coli heat shock
> protein 70 precursor (dnaK) gene, complete cds
>         (1917 letters)
> 
> Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
> GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
>           1,047,083 sequences; -311,112,946 total letters
> 
> Searching... please wait.. done
> 
>                                                                 Score    E
> Sequences producing significant alignments:                      (bits)
> Value
> THEN THE RESULTS.
> 
> Why is the value negitive in total letters (1,047,083 sequences; -
> 311,112,946
> total letters)? It is very hard to parse the blastoutput using bioperl for
> the
> negetive value. Morever when i submitted the query directly on your
> webpage I
> get 3,778,900 sequences; 16,763,624,885 total letters.
> Why is this difference do we missout sequence when we run blastcl3? What
> has
> to be done so that negetive doesnot come on the blastoutput.
> 
> Thanking you
> 
> --
> Sanjib Kumar Gupta
> Bioinformatics Centre
> Bose Institute
> Kolkata 700054, INDIA
> Phone  : +91-33-2334 6626, 2816, 2358 4766
> Fax    : +91-33-2334 3886
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