[Bioperl-l] no results with standalone tblastn

[Torsten Seemann]

> I have downloaded all the databases, as you recommended me. And it is 
> working, but I don't get any results, if I try it online it works fine.
> my result file looks like that:
> 
> TBLASTN 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=
>          (8 letters)
> Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
> GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
>            3,749,503 sequences; 16,556,997,203 total letters
> Searching..................................................done
> Sequences producing significant alignments:                Score    
> E      (bits) Value

Is your query only 8 amino acids long?

This report looks like it did have alignments that were not displayed, 
otherwise it would print "**** No hits ****".

This mailing list is not here to solve your BLAST problems unless it is 
a problem with the Perl module running BLAST.

You first need to try and get your problem working on the command line 
*without* Perl. eg.

/home/Hubert/blast/blast-2.2.13/bin/blastall -p tblastn -d nt -i 
YOUR_FASTA_FILE_WITH_SEQUENCE_IN_IT -o OUTPUT_FILE.txt -e 0.001
...

where "..." is the rest of the options you are setting in your Perl 
script. If it doesn't work that way, it will never work in Perl.

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/