This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Data File Which Maps Between Gene Names and Uniprot Protein IDs

Hello,

I am looking for a data file, which provides mappings between Gene Names and Uniprot Protein IDs. For example, entering ERN2 refers to Q76MJ5 when entered into Uniprot's website.

Thanks

gene-name mapping uniprot

4 answers

Have a look at Ensembl's Biomart. In attributes, select associated gene name and UniProt/SwissProt ID.

Why don't you use the www.uniprot.org search functionality and using the columns button and download in format tab-delimited to get a list of UniProt Acc\tGene Name? e.g. http://www.uniprot.org/uniprot/?limit=10&force=no&format=tab&columns=id,genes

This you can then use in any tool of your own design.

If you have access to the UniProt blast database you can grab them using blastdbcmd.

A word of caution: UniProt does a good job of standardizing symbols (what you're referring to) as well as short and full names, within UniProt. It can be difficult getting complete mapping if you're using non-standard symbols or naming.

If the use of the UniProt website as proposed above doesn't suit you, you might also consider proceeding as described here.

Log in to answer this question.