Database Error When Running Blastn

Question

[Anima Mundi]

Hello, as initially stated No Alignment In The Output Of Blastn, I am experiencing problems when I try to run the blastn command blastn -query myquery -db mydatabase.fasta.nhr.

What I get is:

BLAST Database error: No alias or index file found for nucleotide database [mydatabase.fasta.nhr] in search path [/home/user/Desktop::]

The database file was generated using makeblastdb -in mydatabase.fasta -dbtype nucl, which actually outputs three files, all giving the same error as above.

I understand that somehow I should add an external "alias or index" file in the same folder, maybe the solution would require blastdb_aliastool, included in the BLAST command line user manual, but at this point I would appreciate some hints. Thanks in advance.

[Sudeep]

Did you try running blastn -query myquery -db mydatabase.fasta without .nhr suffix ? I suppose that your sequence database name is mydatabase.fasta

[Michael]

You could create an alias db using blastdb_aliastool to make an alias, use cases are to either define a subset of a db by GIs (e.g. swissprot is an alias of NR), or make a compound db out of several existing dbs. In your case you don't need to do this nor create any more files, but follow Sudeep's suggestion. You normally do not need to care much about the individual database files unless you want to distribute them.

[Anima Mundi]

Thanks a lot guys. In effect I always tried to use one of those three files generated by makeblastdb as database. It works fine now.