Question: Data File Which Maps Between Gene Names and Uniprot Protein ID's
0
gravatar for pwg46
4.7 years ago by
pwg46370
United States
pwg46370 wrote:

Hello,

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

Thanks

 

mapping file uniprot data gene name • 1.7k views
ADD COMMENTlink modified 4.7 years ago by Elisabeth Gasteiger1.6k • written 4.7 years ago by pwg46370
3
gravatar for Jean-Karim Heriche
4.7 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

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

ADD COMMENTlink written 4.7 years ago by Jean-Karim Heriche21k
0
gravatar for me
4.7 years ago by
me690
Switzerland
me690 wrote:

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.

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by me690
0
gravatar for pld
4.7 years ago by
pld4.8k
United States
pld4.8k wrote:

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.

ADD COMMENTlink written 4.7 years ago by pld4.8k
0
gravatar for Elisabeth Gasteiger
4.7 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

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

http://www.uniprot.org/help/gene_symbol_mapping

ADD COMMENTlink written 4.7 years ago by Elisabeth Gasteiger1.6k
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