No Alignment In The Output Of Blastn
Hello everybody, I am trying to BLAST a nucleotide query against a nucleotide database via command line.
The problem is that, when I try blastall -p blastn -d mydatabase -i myquery I get just:
BLASTN 2.2.25 [Feb-01-2011]
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= myquery
(52 letters)
Nothing else is displayed, even when trying to make positive control experiments. What is wrong?
Thanks in advance.
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Have you tried blasting your sequences on ncbi server? Just to check if they are ok.
I just tried, it works on NCBI.
Consider this answer - A: Help with formatdb and blast all (
blastallvsblastn)Thanks; actually, I was trying to use blastall to avoid a problem in the format of my subject database while using blastn. Maybe I will open a new question to fix that issue.
Here is the new question: Database error when running blastn