Question: Retrieving accession numbers using locus tags with blastdbcmd or others tools?
gravatar for courtney.stairs
3.3 years ago by
courtney.stairs0 wrote:

I have a list of locus tags used in a publication and I would like to match these to the protein accession number. I could write a script to do this by parsing the GenBank pages for the genome, but I was hoping there was a tool out there! For locus tag: SS50377_14631 I tried blastdbcmd:

blastdbcmd -outfmt %a -entry 'SS50377_14631' -db /local/one/databases/nr

and got the following error:

Error: [blastdbcmd] SS50377_14631: OID not found
Error: [blastdbcmd] SS50377_14631: OID not found
BLAST query/options error: Entry or entries not found in BLAST database
Please refer to the BLAST+ user manual.

But this locus tag does work on the genbank webpage to retrieve protein EST43027.1

Thank you for your help!

blast gene • 1.1k views
ADD COMMENTlink written 3.3 years ago by courtney.stairs0

The tag you posted brings back two entries via Entrez search. This Nucleotide WGS genomic scaffold and this protein entry.

The connection between the locus tag above must be made internally at NCBI via some other means.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by genomax72k
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