[Bioperl-l] help on blastcl3

Sanjib Kumar Gupta sanjib at bic.boseinst.ernet.in
Fri Mar 10 03:15:41 EST 2006


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

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 
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

More information about the Bioperl-l mailing list