BLAST database error: no alias or index file found for nucleotide database [swissprot] in search path.....
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6.9 years ago
arfaj a ▴ 10

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 mean?

I follow the link step by step.

Any hints?

Thank you and regards,
Alaa

blast • 4.3k views
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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.

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