Question

Blast Can'T Find Databases

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Entering edit mode

13.1 years ago

Jesse J ▴ 150

I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has

[BLAST]
BLASTDB=/home/bioinformatics/Desktop/blastDB

and yet when I try to run blastn I get this:

blastn -query Desktop/sea_urchin_output1/permutations.fa -db nr
BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/bioinformatics::/home/bioinformatics/Desktop/blastDB:]

I've tried following instructions to get this to run, but it still doesn't work. Is there something I'm missing?

blastn blast • 21k views

ADD COMMENT • link updated 8.4 years ago by arafelyb8 • 0 • written 13.1 years ago by Jesse J ▴ 150

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Entering edit mode

What you were told to use and what is correct may not be the same thing :) According to http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdb.html the non-redundant nucleotide database files are still called nt.*.tar.gz. If you are using blastn then you want nt, not nr (which is proteins).

ADD REPLY • link 13.1 years ago by Neilfws 49k

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Two thoughts. (1) Have you checked that /home/bioinformatics/Desktop/blastDB contains the required files, their sizes look right and their names all begin with nr.*? (2) Are you sure that nr is the correct database? For blastn, you should be using the nucleotide database, which was named nt the last time I used it.

ADD REPLY • link 13.1 years ago by Neilfws 49k

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Yes and yes. The files are there and blastn with nr is what I was told to use.

ADD REPLY • link 13.1 years ago by Jesse J ▴ 150

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Just guessing: did you unzip the .tar.gz file?

ADD REPLY • link 13.1 years ago by Michael Schubert ★ 7.1k

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Nice it worked for me! However I wonder an error message as "blasn expected nucleotides database" to realize i'm not using the correct blast. Thanks

ADD REPLY • link 8.4 years ago by arafelyb8 • 0

score 7 · Answer 1 · 2011-11-12

Assuming you have untarred and ungzipped it correctly, the problem is reported correctly, but is not obvious to the beginner:

No alias or index file found for nucleotide database [nr]

You see, "nr" is a PROTEIN database. It's indices are stored in the "nr.pin" file. Note the "p" in pin. Because you are using blastn, which is nucleotide query VS nucleotide database, it is looking for a "nr.nin" index file, not the "nr.pin" you have.

You either need to install "nt", or use "blastx -db nr" instead, which will translate your query in six frames and match against the nr proteins.