[ensembl-dev] pfam domain on human ensembl proteins

[Bronwen Aken]

Hi Venu,

Yes, we do display Pfam domains for all Ensembl proteins.

There are a few ways for you to access the data depending on your preference.

1. Core API: 
eg. $pfam_features = $translation->get_all_ProteinFeatures('PFam');


2. BioMart:
eg. Select the gene or list of genes that you are interested in and then select the attributes / features (eg. PFAM IDs) that you are interested in.




3.Website. On the website, you can find this under the "Protein information" section of our left-hand menu. For example:

http://e73.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000544455



http://www.ensembl.org/Homo_sapiens/Transcript/Domains?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000544455



4. Finally, our public MySQL server
 mysql -NB -uanonymous -P3306 -hensembldb.ensembl.org -Dhomo_sapiens_core_73_37 -e "select hit_name,pf.seq_start,pf.seq_end from transcript t, translation tln, protein_feature pf, analysis a where a.analysis_id = pf.analysis_id and t.transcript_id=tln.transcript_id and tln.translation_id=pf.translation_id and t.stable_id = 'ENST00000380152' and logic_name='pfam'"
PF09169 2479    2667
PF00634 1002    1036
PF00634 1212    1246
PF00634 1421    1454
PF00634 1517    1550
PF00634 1664    1696
PF00634 1837    1869
PF00634 1972    2005
PF00634 2051    2084
PF09104 3052    3190
PF09103 2670    2799
PF09121 2831    2872


Hope that helps,
Bronwen


On 11 Sep 2013, at 23:05, Venugopal Valmeekam <vvalmeekam at yahoo.com> wrote:

> Hi,
> Could you please let me know if ensembl provides pfam domains mapped to ensembl protein coordinates?  I mean does ensembl run HMMER on ensembl protein collection using pfam HMMs?  I am interested in the ensembl human protein collection.  I know that pfam provides this data for uniprot and ncbi nr proteins, but often these proteins don't match exactly with ensembl protein sequences.
> thanks,
> Venu
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