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From RefSeq to Go Terms

My aim is getting the list of GO terms for a big list of genes (~250000).

The genes belong to genomes of bacteria downloaded from RefSeq, so they have this kind of identifiers: NP_953938.1.

I guess the solution should be using BioMart. However, the database of RefSeq is not included in the ones you can parse with it.

I tried then to retrieve the Entrez IDs from this file: ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq

But some of them (I think most of them) do not appear in the document, e.g. WP_013258072.1

Any other ideas? How can I get the GO terms from the RefSeq IDs?

go refseq biomart
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updated by Ram Ram • written by aaredav • aaredav

What bacteria are we talking about?

biomartian --list-datasets | grep -i bac

Returns no results, so I am guessing it is not a part of ensembl.

I guess the solution should be using BioMart. However, the database of RefSeq is not included in the ones you can parse with it.

Can you reformulate this sentence?

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updated by Ram Ram • written by Endre Bakken Stovner Endre Bakken Stovner

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