error in Makeblastdb

Question

[Janey]

Hi

I want to make local database by uniref90 with this command:

./makeblastdb -in uniref90.fasta -dbtype prot -out uniref_db

but i get multiple psq, pin and phr files:

uniref_db.09.psq

uniref_db.09.pin

uniref_db.09.phr

uniref_db.08.psq

uniref_db.08.pin

uniref_db.08.phr

........................

Can anyone help me to solve this problem.

Answer 1

[Joe]

Its not a problem, its normal. The database is very large, so makeblastdb breaks it up.

On our server, the nr database is in 83 parts for example. You only ever need to provide the 'stem name' of the database to blast, as it uses all the various extensions, so it will find the mulitple parts as normal.

In your case, you'd do something like:

blast -db /path/to/uniref_db   <options>    # note that the extension isnt specified for the DB.

[Janey]

Thank you for your answer.

[WouterDeCoster]

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