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How To Generate Blast Database

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

dataset blast database genome
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updated by Xingyu Yang Xingyu Yang • written by Ongkrab • Ongkrab

1 answer

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
• 143 views • link
written by Xingyu Yang Xingyu Yang

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