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blastn cannot find the database

I'm new to BLAST and am trying to run a legacy blast command using blast+. I have downloaded the human_genome databases and unzipped and untarred them.

The databases are in: /home/assay/assay/bin/blast/db/human_genomic

They look like this:

human_genomic.01.nsd  human_genomic.03.nsd  human_genomic.05.nog  human_genomic.07.nni  human_genomic.09.nnd  human_genomic.11.ninhuman_genomic.01.nsi  human_genomic.03.nsi  human_genomic.05.nsd  human_genomic.07.nog  human_genomic.09.nni  human_genomic.11.nn human_genomic.00.nhd  human_genomic.01.nsq  human_genomic.03.nsq  human_genomic.05.nsi  human_genomic.07.nsd  human_genomic.09.nog  human_genomic.11.nni  .... etc ...

There is also a human_genomic.nal file in the directory

The command line I am using & error message is:

$  ./legacy_blast.pl blastall -p blastn -d human_genomic -m 7 -q -2 -W 7 -e 1000 -F T
BLAST Database error: No alias or index file found for nucleotide database [human_genomic] in search path [/home/assay/assay/bin/blast/bin:/home/assay/assay/bin/blast/db:]
Program failed, try executing the command manually.
blast
• 3,611 views • link
updated by Ram Ram • written by sfcarroll • sfcarroll

I should note I am trying to blast results from Primer 3, which was run against hg19. Do I have the right database: human_genomic ?

• 0 views • link
written by sfcarroll • sfcarroll

1 answer

I resolved it.

The database path needs to include the name of the database directory.

Full command line:

/home/assay/assay/bin/blast/bin/legacy_blast.pl blastall -p blastn -d /home/assay/assay/bin/blast/db/human_genomic -m 7 -q -2 -W 7 -e 1000 -F T
• 0 views • link
updated by Ram Ram • written by sfcarroll • sfcarroll

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