How To Generate Blast Database

Question

[Ongkrab]

Hello I downloaded some database in gemnomes/Bacteria ( ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Acetobacterium_woodii_DSM_1030_uid88073/ ) I want to use blast program. I have some problem.

How can I generate Acetobacterium_woodii_DSM_1030_uid88073 database in local Blast. I use in ubuntu. In fact, I want to use only Bacteria database for use standalone blast.

Thank you very much

[Michael]

Please Read The Fine Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ refer to section on makeblastdb.

Answer 1

[Xingyu Yang]

First, download the reference file in fasta format. If you want to use protein, download those end with .faa;if nucleotide, download those end with .fna.

Then, you can build the index. Which command to do this depends on which version of blast you use.

If you use blastall,

formatdb --help

If you use blast+

makeblastdb -help