Question: Hgnc To Uniprot
0
gravatar for cdsouthan
6.3 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

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

mapping • 3.2k views
ADD COMMENTlink modified 6.3 years ago by Fred730 • written 6.3 years ago by cdsouthan1.8k
1

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

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

ADD REPLYlink written 6.3 years ago by Neilfws48k

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)

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by cdsouthan1.8k

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

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by cdsouthan1.8k

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

ADD REPLYlink written 6.3 years ago by cdsouthan1.8k

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

ADD REPLYlink written 6.3 years ago by Rm7.9k

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

ADD REPLYlink written 6.3 years ago by cdsouthan1.8k
1
gravatar for Fred
6.3 years ago by
Fred730
Paris, France
Fred730 wrote:

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.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Fred730
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