BLAST database index file

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4.8 years ago

bioinf_sci ▴ 20

When attempting to run protein BLAST locally against the nr database (downloaded from https://www.ncbi.nlm.nih.gov/public/ ) I get an error stating that I need an index file. Do I need to run makeblastdb on this file before I can use it? Should I download the nr database elsewhere? Thanks!

BLAST • 916 views

ADD COMMENT • link updated 4.7 years ago by Biostar 20 • written 4.8 years ago by bioinf_sci ▴ 20

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You can download it here ftp://ftp.ncbi.nlm.nih.gov/blast/db/ pre-formatted. You can also use the update_blastdb.pl tool.

ADD REPLY • link 4.8 years ago by gb ★ 2.2k

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Thank you. Realized it's a firewall issue not allowing me to access the ftp site which is why I searched for the database elsewhere.

ADD REPLY • link 4.8 years ago by bioinf_sci ▴ 20

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You need to download all nr* files from the database link posted by @gb. Uncompress and store them in one folder.

What you downloaded from the link you posted in original post are just fasta formatted files for nr.

ADD REPLY • link 4.8 years ago by GenoMax 147k

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