Retrieve nucleotide ID from protein ID
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2.1 years ago
kmears • 0

Hello,

I have a list of proteins for which I need to find the corresponding nucleotide sequences. For example find NC_001498 from NP_056922.1. I figure there should be an easy way to do this but I'm not familiar with the ins and outs of Entrez/biopython.

Thanks!

refseq entrez bipython • 722 views
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2.1 years ago
vkkodali_ncbi ★ 3.7k

You can use EntrezDirect for this as follows:

$ epost -db protein -id NP_056922.1 | elink -target nuccore | efetch -format acc
NC_001498.1

Alternatively, you can use Batch Entrez to upload your list of protein accessions, retrieve the proteins and then using the "Find related data" widget on the right-hand side to get a list of all related Nucleotide records.

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Thank you, is there an easy way to do this with python as well?

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Yes, take a look at Bio.Entrez. Personally though, I just find it easier to use subprocess module in python and run the EntrezDirect commands within the python script... but that may not always be feasible.

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