[Bioperl-l] no results with standalone tblastn
torsten.seemann at infotech.monash.edu.au
Mon Feb 6 21:17:40 EST 2006
> 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.
> (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
> 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.
Victorian Bioinformatics Consortium, Monash University, Australia
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