What are the makeblastdb database files doing?

Question

[timothy.kirkwood]

Hi All,

I'm doing some local BLASTS with BLAST+ v2.10.1 and was wondering if anyone could tell me what the database files actually are/do - they are made using makeblastdb with a fasta file and the suffixes are: .pdb, .phr, .pin, .pot, .psq, .ptf, .pto.

Also, I assume BLAST+ does this automatically, but is there any way to speed up blast using these? I currently just set the database as whatever the file name is up to the suffix above - so for example, if I have files mydb.pdb, mydb.phr, mydb.pin, mydb.pot, mydb.psq, mydb.ptf and mydb.pto, I will set the database flag as 'file/path/to/mydb' (with no suffix). Is there any way to use these files to speed up the BLAST search (e.g. with one of the many blast cmd flags) or does BLAST do this all as fast as possible automatically?

Cheers!

Answer 1

[Mensur Dlakic]

makeblastdb makes index files from a database of protein or DNA sequences. Their purpose is to speed up the search and they are used automatically by an appropriate BLAST program. In fact, once you create those index files, you don't need the original FASTA files as far as BLAST is concerned.

[timothy.kirkwood]

Perfect, thanks for the answer!