Is it possible to pull Genbank ID from RefSeq?
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21 months ago
anabaena • 0

Hey everyone, I have a list of RefSeq protein ID's and need to pull the GenkBank/INSDC data. When I pull the attached data to the RefSeq WP_XXXXX either through esummary, or elink I get no connection to anything else not even the WGS data, so I was wondering if it was even possible to do so in Biopython Entrez?

Entrez Biopython • 381 views
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21 months ago
GenoMax 108k

With Entrezdirect you could do something like this:

$ esearch -db protein -query "WP_060189833.1" | elink -target nuccore | efetch -format acc
NZ_LPHR01000079.1
NZ_LPKX01000035.1
NZ_LPBZ01000030.1
NZ_MEBG01000045.1

These are GenBank ID's but they refer to genome sequences.

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Awesome thanks! I am assuming these commands can be translated into Biopython? as I need to iterate over a large list?

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Yes. Should be possible.

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