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I am attempting to run a BLAST search remotely using BLAST+.

I can get search to work correctly at the command line with the following commands:

blastp -query proteins.fasta -remote -db nr -out proteins_nr.txt -outfmt 6 -evalue 1e-30

However, I would like to us the remote database titled "Microbial proteins from nr" which is what would be used for the microbial blast search accessing BLAST from the NCBI site.

I'm struggling to find the correct code to access this database instead of just "nr".

Is there a list with the codes of different databases?

Thanks in advance

bluescholar1212
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1 Answers1

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I believe you're looking for env_nr? It's listed as such, under Metagenomic proteins in the blastp webpage. It appears that the word within brackets should be supplied alongside the -db parameter. A quick test with a dummy amino acid fasta file does turn up a result to a valid NCBI protein accession.

partial screenshot from NCBI's blastp webpage

Edit: I followed up on this with a little more digging around, and it appears the database you're looking for is called Microbial_proteins. I ended up quote-searching Microbial proteins from nr on Google and exactly 2 hits turn up. The first hit, I think, is what the OP posted a screenshot of in a comment to this answer. The second is a list of databases along with keywords from a Spain-based bioinformatics firm: http://data.biobam.com/ncbi_blast_dbs_protein.pdf. I retried the dummy example with the Microbial_proteins database, and it seems to work. Again, I am not sure why I can't easily find this on an NCBI resource. Also, I am curious as to how different this database is from env_nr.

flatley176
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  • @flatley176 thank you for response. That answers what I can specify with -db. Unfortunately I'm not looking to blast against env_nr. I would like to blast against the website database using blast+ and specify this database:

    Valid XHTML

    is there a way to specify this for a -remote blast using blast+

    thank you.

     – bluescholar1212 Jun 24 '17 at 20:07
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    I do not know how Microbial proteins from nr differs from the env_nr database. Page 3 of the BLAST manual (ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLASTGuide.pdf) lists the available databases - the only reference to the word "microbial" is to the 16s rRNA. That said, I dug around a little more, and it appears there IS a solution - the database is called Microbial_proteins. Will update my answer. – flatley176 Jun 25 '17 at 07:16