Question: Finding Human DUFs
0
gravatar for cdsouthan
3 months ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

As as an exercise for evaluating Phyre I wanted to look at human proteins with neither obvious structure nor established function. Now Pfam does have DUFs (domains of unknown function) nested in this data sheet in fact http://pfam.xfam.org/family/browse?browse=d. However, in the UniProt interface wild cards do not work hence database:(type:pfam id:DUF*) wont do. Any ideas for finding which human Swiss-Prots contain a DUF?

ADD COMMENTlink modified 3 months ago • written 3 months ago by cdsouthan1.8k
2

You should get a list of all human proteins in UniProt containing DUF domains using this query: annotation:(type:"positional domain" duf) AND organism:"Homo sapiens (Human) [9606]"

ADD REPLYlink written 3 months ago by a.zielezinski8.3k

Where does this run please? Uniprot interface says bad syntax and I cant see those selects in the options

ADD REPLYlink modified 3 months ago • written 3 months ago by cdsouthan1.8k

Thanks a lot, actually this ran - annotation:(type:"positional domain" duf) AND reviewed:yes AND organism:"Homo sapiens (Human) [9606]" Only gave 7 results but was not expecting much. Simple, when you know how :)

ADD REPLYlink modified 3 months ago • written 3 months ago by cdsouthan1.8k

In addition to 7 reviewed proteins (UniProt/SwissProt), you have also 653 unreviewed proteins. Here is the link.

ADD REPLYlink written 3 months ago by a.zielezinski8.3k

Thanks, but JFTR these are just TrEMBL bits and bobs

ADD REPLYlink written 3 months ago by cdsouthan1.8k
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