This seems like it may be well-worn territory, but I have many lists of protein accession numbers that are in text files in a column (from 330 to 20000 accession numbers). I would like to get the organism names for these proteins, but I'm not sure how. Any suggestions?
Thanks
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written
by
kgbenn123 •
2 answers
You can use here Batch Entrez tool (https://www.ncbi.nlm.nih.gov/sites/batchentrez) to retrieve the record from NCBI database. Save all these accession numbers in a text file and submit it as a query (using browse button) and retrieve the records. In your case, you can select a nucleotide or any other appropriate database as per your requirement. If you are good in programming, I suggest you to use Biopython.
You can also get the organism from accessions like this:
http://taxonomy.jgi-psf.org/tax/accession/ELW65244.1,XP_013802631.1
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show us some accession numbers please.
I forgot to make this a reply to your comment so now there are two copies...
Here are 29 numbers from one of the datasets I'm working with:
ELW65244.1
XP_013802631.1
KYB28707.1
CRK95935.1
KHN78054.1
ENN75534.1
XP_017304189.1
XP_014597100.1
XP_006140718.1
XP_016061608.1
OBS71931.1
ELK37553.1
XP_007099480.1
XP_006022987.1
XP_005633823.1
XP_008147166.1
KFO26429.1
AAM94168.1
EHB17201.1
XP_008539104.1
XP_008947951.1
EMP28105.1
XP_018423279.1
XP_015194130.1
XP_005991276.1
XP_018112941.1
XP_020651304.1
XP_018618676.1
CAF99922.1
Here are 29 numbers from one of the datasets I'm working with:
ELW65244.1
XP_013802631.1
KYB28707.1
CRK95935.1
KHN78054.1
ENN75534.1
XP_017304189.1
XP_014597100.1
XP_006140718.1
XP_016061608.1
OBS71931.1
ELK37553.1
XP_007099480.1
XP_006022987.1
XP_005633823.1
XP_008147166.1
KFO26429.1
AAM94168.1
EHB17201.1
XP_008539104.1
XP_008947951.1
EMP28105.1
XP_018423279.1
XP_015194130.1
XP_005991276.1
XP_018112941.1
XP_020651304.1
XP_018618676.1
CAF99922.1