error when running blastn
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Entering edit mode
3.4 years ago
Nifaste ▴ 20

Dear biostars community,

I encountered a problem when running a blast on my computer. I downladed nr database from ncbi ftp (all the nr.**.tar.gz files). then, I unzip each of the 131 files. All the file are in /root/nr directory. I add this directory to $BLASTDB with

export BLASTDB='/root/nr'

And run :

blastn -query '/root/tmp.fasta' -db nr

But i have the following error message :

BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/root:/root/nr:]

I have the nr.pal file, taxdb.btd, taxdb.bti and all file for each subset of the database.

Any recommandation ?

Thanks in advance for your help

blast alignment blastn • 743 views
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my mistake, blastn is for nucleotide and nr is proteic sequence :(

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3.4 years ago

You may wish to try BIRCH, a comprehensive bioinformatics package, which includes desktop tools for installing and managing local copies of BLAST, and doing BLAST searches, automated through our BioLegato applications.

BLAST is demonstrated in a recent video: BIRCH - Desktop Bioinformatics (long version)

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