Question: BLAST database error: no alias or index file found for nucleotide database [swissprot] in search path.....
0
gravatar for arfaj a
3.3 years ago by
arfaj a10
arfaj a10 wrote:

Hello everyone,

I am following this link: http://www.ncbi.nlm.nih.gov/books/NBK52637/

I install NCBI BLAST+ package. Then create db folder inside blast-2.2.31+ folder to download one of NCBI databases. I select swissprot database and download it in the db folder. After that, I run:

perl update_blastdb.pl --passive swissprot

and it connect to NCBI successfully and download swissport in the bin folder. So, now I have two swissprot.tar.gz. One I download it in db folder and one downloaded in bin folder after running perl cammand.

 

Then I set PATH and BLASTDB environment variables. BLASTDB will contain which swissport database? the one in db or in bin?

 

The main issue appears when I type:

blastdbcmd -db swissprot -info

BLAST database error: no alias or index file found for nucleotide database [swissprot] in search path.....

What does this means?

I follow the link step by step.

 

Any hints?

Thank you and regards,,,

Alaa

 

blast • 2.8k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 3.3 years ago by arfaj a10
2

Did you uncompress the swissprot.tar.gz? Once you do that it should produce several individual files with extensions like .pin, .phr, .phq etc. Then your blastdbcmd command should work.

ADD REPLYlink written 3.3 years ago by genomax64k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 829 users visited in the last hour