Hgnc To Uniprot

Question

[cdsouthan]

None of the web interfaces I have tried for HGNC Symbol list to SwissProt have produced a clean I:I human conversion. Any suggestions ?

[Neilfws]

Examples of which services you have tried? And example HGNC symbols with resulting SwissProt entries?

Also, why are you expecting a 1:1 match?

[cdsouthan]

The problems in the otherwise exellent UniProt interface is it needs the HGNC IDs (not symbols alone) so I have to a) use the HGNC site to generate these from a symbol list and b) it cross-species converts by default so I have to restrict to human afterwards. The mappings should be 1:1 (and are for ~ 19K) but HGNC and UniProt need to curatorialy finish the job (along with Ensembl genes NCBIs EGIDs as well for 1:1:1:1)

[cdsouthan]

PICR works but a) slowly b) the Excell downloads are very quirky at my end and c) for "best guess UniProt" I then have to strip off all the version numbers

[cdsouthan]

From HGNC queries I have UniProt download option but I cant simply upload a list for conversion

[Rm]

did you tried this: http://www.uniprot.org/database/DB-0042

[cdsouthan]

Yes, I can get the full download lists, its just I didnt want to have to intersect all 19,694 if I have just had a few hundred HGNC symbols to map from a supplimentary data sheet

Answer 1

[Fred]

What about using the HGNC custom download ?

And only selecting HGNC ID, Approved Symbol and UNIPROT ID?

Here is an example of a link generated that way.

You can then filter the list as you want.