Download peptide sequences from NCBI using python

Question

[יובל]

I would like to extract the peptide sequence of the following: NM_021969.2 from the NCBI website as shown in this link: https://www.ncbi.nlm.nih.gov/nuccore/NM_021969.2

I was able to extract the nucleotide sequence using the following script, but I am unable to extract the following peptide sequence:

MSTSQPGACPCQGAASRPAILYALLSSSLKAVPRPRSRCLCRQH                  RPVQLCAPHRTCREALDVLAKTVAFLRNLPSFWQLPPQDQRRLLQGCWGPLFLLGLAQ                     DAVTFEVAEAPVPSILKKILLEEPSSSGGSGQLPDRPQPSLAAVQWLQCCLESFWSLE                     LSPKEYACLKGTILFNPDVPGLQAASHIGHLQQEAHWVLCEVLEPWCPAAQGRLTRVL
LTASTLKSIPTSLLGDLFFRPIIGDVDIAGLLGDMLLLR

Python script:

Entrez.email = '[e-mail]'

handle = Entrez.efetch(db='nuccore', id='NM_021969.2', rettype='fasta')

print(handle.read())

I would appreciate some help if anyone has succeeded.

Yuval

Answer 1

[iraun]

Hi! Welcome to Biostars :).

Try this:

Entrez.efetch(db="protein", id='NM_021969.2',  rettype="fasta")

[יובל]

Thanks for your help, it solved my problem.

[Ram]

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Answer 2

[MirianT_NCBI]

Hi,
You can use NCBI Datasets. To download the protein sequence associated with this nucleotide record, you can use the following command:

datasets download gene accession NM_021969.2 --include protein

This command will download a zip file, with the following contents:

ncbi_dataset
`-- data
    |-- data_report.jsonl
    |-- dataset_catalog.json
    `-- protein.faa

By default, NCBI Datasets gene data package includes transcript and protein sequences, as well as metadata as JSON-Lines. You can include other files (if available) using the flag --include, as exemplified above.

Feel free to reach out if you have any additional questions. I hope it helps :)