Question: No Alignment In The Output Of Blastn
0
gravatar for Anima Mundi
5.1 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

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.

blastn blast command-line • 1.5k views
ADD COMMENTlink written 5.1 years ago by Anima Mundi2.4k

Have you tried blasting your sequences on ncbi server? Just to check if they are ok.

ADD REPLYlink written 5.1 years ago by PoGibas4.7k

I just tried, it works on NCBI.

ADD REPLYlink written 5.1 years ago by Anima Mundi2.4k

Consider this answer - A: Help with formatdb and blast all (blastall vs blastn)

ADD REPLYlink written 5.1 years ago by PoGibas4.7k

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.

ADD REPLYlink written 5.1 years ago by Anima Mundi2.4k

Here is the new question: Database error when running blastn

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Anima Mundi2.4k
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