<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Venu,<div><br></div><div>Yes, we do display Pfam domains for all Ensembl proteins.</div><div><br></div><div>There are a few ways for you to access the data depending on your preference.</div><div><br></div><div>1. Core API: </div><div>eg. <span style="background-color: rgb(251, 252, 253); font-family: monospace, fixed; font-size: 9pt; line-height: 15px; ">$pfam_features = $translation->get_all_ProteinFeatures(</span><span class="stringliteral" style="font-family: monospace, fixed; font-size: 1em; line-height: 15px; color: rgb(0, 32, 128); ">'PFam'</span><span style="background-color: rgb(251, 252, 253); font-family: monospace, fixed; font-size: 9pt; line-height: 15px; ">);</span></div><div><br></div><div><br></div><div>2. BioMart:</div><div>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.</div><div><br></div><div><img height="322" width="602" apple-width="yes" apple-height="yes" id="a315a5b4-f4fb-42f9-a6af-4ca01712f34a" src="cid:139A432E-CBE5-425E-92B8-7F0103D20891@internal.sanger.ac.uk"></div><div><br></div><div><br></div><div>3.Website. On the website, you can find this under the "Protein information" section of our left-hand menu. For example:</div><div><br></div><div><a href="http://e73.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000544455">http://e73.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000544455</a></div><div><img height="249" width="622" apple-width="yes" apple-height="yes" id="7d4700b6-c622-49ab-9b58-ee66fc46ffef" src="cid:0AA6990D-3D5B-4DC6-904F-862C510EE248@internal.sanger.ac.uk"></div><div><br></div><div><br></div><div><a href="http://www.ensembl.org/Homo_sapiens/Transcript/Domains?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</a></div><div><img height="225" width="916" apple-width="yes" apple-height="yes" id="4373b01f-6ac3-4a64-8300-635a5d0c3d99" src="cid:4143B88F-9520-4822-89B9-ACE301E276D9@internal.sanger.ac.uk"></div><div><br></div><div><br></div><div>4. Finally, our public MySQL server</div><div><div> mysql -NB -uanonymous -P3306 -<a href="http://hensembldb.ensembl.org">hensembldb.ensembl.org</a> -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'"</div><div>PF09169 2479 2667</div><div>PF00634 1002 1036</div><div>PF00634 1212 1246</div><div>PF00634 1421 1454</div><div>PF00634 1517 1550</div><div>PF00634 1664 1696</div><div>PF00634 1837 1869</div><div>PF00634 1972 2005</div><div>PF00634 2051 2084</div><div>PF09104 3052 3190</div><div>PF09103 2670 2799</div><div>PF09121 2831 2872</div></div><div><br></div><div><br></div><div>Hope that helps,</div><div>Bronwen</div><div><br></div><div><br><div><div>On 11 Sep 2013, at 23:05, Venugopal Valmeekam <<a href="mailto:vvalmeekam@yahoo.com">vvalmeekam@yahoo.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="background-color: rgb(255, 255, 255); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><meta charset="utf-8"><div>Hi,</div><div>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.</div><div>thanks,</div><div>Venu</div></div></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br></div></body></html>