[Bioperl-l] help on blastcl3

[Sanjib Kumar Gupta]

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