How to format nr database for blastp?

Question

[MAPK]

Hi All, I am using nr.gz database downloaded from ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz. I am doing this after several years and I don't remember exactly if this is how this should be extracted. So here is what I have tried formatdb -i nr.gz -o T -p T which doesn't seem to work anymore or gives me this error: [formatdb] WARNING: Cannot add sequence number 1 (lcl|1_nr.gz) because it has zero-length.. I would really appreciate if someone could guide me through correct procedure.

[lieven.sterck]

small side note: formatdb is linked to quite old blast versions, nowadays it's replaced by makeblastdb , part of the most recent blast+ versions.

[GenoMax]

Why did you not get the pre-made nr blast indexes from ftp://ftp.ncbi.nih.gov/blast/db/?

[MAPK]

Thanks.. should I just download nr.* then?

[GenoMax]

Yep. That would be the easiest.

[MAPK]

One more question-Do I have to do makeblastdb after I untar all these files? Thanks again!

[GenoMax]

No there is nothing more to do. Just untar all files and make sure they are all in the same directory.

Answer 1

[h.mon]

Use the update_blastdb.pl script to download, check md5sum and decompress blast databases. This script is bundled with BLAST+ download, and on Debian-based systems, if you install BLAST+ from the repository, the script is renamed update_blastdb. To see the available databases:

update_blastdb.pl --showall

To download nr - will automatically check md5sums:

update_blastdb.pl nr

Or to download, check md5sums, decompress and remove gzipped files:

update_blastdb.pl --decompress nr