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Microbial protein BLAST

I am trying to run BLAST online using Biopython: from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast("blastp", "nr", consensus_seq)

How can I search only Microbial proteins, as I would if I used the web-interface at https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes&LINK_LOC=blasttab&LAST_PAGE=blastn

What should I type in place of 'nr'?

blast microbial proteins biopython databases
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updated by user_without_id user_without_id • written by orpita.d • orpita.d

This may not be possible to replicate via Biopython. NCBI does many things differently via their WWW page that are not easy to replicate via command line blast.

Edit: Answer posted below seems to indicate that this may be feasible. OP will need to confirm.

Look to see if you can pass the option -taxids 2 via your command line. This would limit the search to bacteria.

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written by GenoMax GenoMax

1 answer

I think this works, please check for false positives:

from Bio.Blast import NCBIWWW
# https://www.uniprot.org/uniprot/P21515
consensus_seq = "MNFLAHLHLAHLAESSLSGNLLADFVRGNPEESFPPDVVAGIHMHRRIDVLTDNLPEVREAREWFRSETRRVAPITLDVMWDHFLSRHWSQLSPDFPLQEFVCYAREQVMTILPDSPPRFINLNNYLWSEQWLVRYRDMDFIQNVLNGMASRRPRLDALRDSWYDLDAHYDALETRFWQFYPRMMAQASRKAL"
url = "https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_SPEC=MicrobialGenomes"
result_handle = NCBIWWW.qblast("blastp", "nr", consensus_seq, url_base=url)
print(result_handle.read())
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written by user_without_id user_without_id

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