Difference between revisions of "PFAM"
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| + | <p>The <strong>Pfam</strong> database contains information about protein domains and families. Pfam-A is the manually curated portion of the database that contains over 9,000 entries. For each entry a protein sequence alignment and a hidden Markov model is stored. These hidden Markov models can be used to search sequence databases with the HMMer package written by Sean Eddy. Because the entries in Pfam-A do not cover all known proteins an automatically generated supplement is provided called Pfam-B. Pfam-B is derived from the PRODOM database.</p> | ||
| + | <p>The database <strong>iPfam</strong> builds on the domain description of Pfam. It investigates if different proteins described together in the protein structure database PDB are close enough to potentially interact.</p> | ||
| + | <p> </p> | ||
| + | <h2><span class="mw-headline">See also</span></h2> | ||
| + | <ul> | ||
| + | <li>TrEMBL Database performing an automated protein sequence annotation </li> | ||
| + | <li>InterPro Integration of protein domain and protein family databases </li> | ||
| + | </ul> | ||
| + | <p> </p> | ||
| + | <h2><span class="mw-headline">References</span></h2> | ||
| + | <ul> | ||
| + | <li><cite style="FONT-STYLE: normal">Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006). "Pfam: clans, web tools and services". <em>Nucleic Acids Res.</em> <strong>34</strong>: D247-D251. PMID 16381856.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Pfam%3A+clans%2C+web+tools+and+services&rft.jtitle=Nucleic+Acids+Res.&rft.date=2006&rft.volume=34&rft.au=Finn+RD%2C+Mistry+J%2C+Schuster-Bockler+B%2C+Griffiths-Jones+S%2C+Hollich+V%2C+Lassmann+T%2C+Moxon+S%2C+Marshall+M%2C+Khanna+A%2C+Durbin+R%2C+Eddy+SR%2C+Sonnhammer+EL%2C+Bateman+A&rft.pages=D247-D251"> </span> </li> | ||
| + | </ul> | ||
| + | <ul> | ||
| + | <li><cite style="FONT-STYLE: normal">Finn RD, Marshall M, Bateman A (2005). "iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions". <em>Bioinformatics</em> <strong>21</strong>: 410-412. PMID 15353450.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=iPfam%3A+visualization+of+protein-protein+interactions+in+PDB+at+domain+and+amino+acid+resolutions&rft.jtitle=Bioinformatics&rft.date=2005&rft.volume=21&rft.au=Finn+RD%2C+Marshall+M%2C+Bateman+A&rft.pages=410-412"> </span> </li> | ||
| + | </ul> | ||
| + | <ul> | ||
| + | <li><cite style="FONT-STYLE: normal">Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004). "The Pfam protein families database". <em>Nucleic Acids Res.</em> <strong>32(Database issue)</strong>: D138-D141. PMID 14681378.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The+Pfam+protein+families+database&rft.jtitle=Nucleic+Acids+Res.&rft.date=2004&rft.volume=32%28Database+issue%29&rft.au=Bateman+A%2C+Coin+L%2C+Durbin+R%2C+Finn+RD%2C+Hollich+V%2C+Griffiths-Jones+S%2C+Khanna+A%2C+Marshall+M%2C+Moxon+S%2C+Sonnhammer+EL%2C+Studholme+DJ%2C+Yeats+C%2C+Eddy+SR&rft.pages=D138-D141"> </span> </li> | ||
| + | </ul> | ||
| + | <p> </p> | ||
| + | <h2><span class="mw-headline">External links</span></h2> | ||
| + | <ul> | ||
| + | <li>Pfam - Protein family database at Sanger Institute UK </li> | ||
| + | <li>Pfam - Protein family database at Janelia Farm Research Campus USA </li> | ||
| + | <li>Pfam - Protein family database at Center for Genomics and Bioinformatics Sweden </li> | ||
| + | <li>iPfam - Interactions of Pfam domains in PDB </li> | ||
| + | </ul> | ||
| + | <div class="boilerplate metadata" id="stub"></div> | ||
| + | <p><br clear="all" /> | ||
| + | </p> | ||
| + | </font> | ||
Latest revision as of 21:35, 13 December 2007
The Pfam database contains information about protein domains and families. Pfam-A is the manually curated portion of the database that contains over 9,000 entries. For each entry a protein sequence alignment and a hidden Markov model is stored. These hidden Markov models can be used to search sequence databases with the HMMer package written by Sean Eddy. Because the entries in Pfam-A do not cover all known proteins an automatically generated supplement is provided called Pfam-B. Pfam-B is derived from the PRODOM database.
The database iPfam builds on the domain description of Pfam. It investigates if different proteins described together in the protein structure database PDB are close enough to potentially interact.
See also
- TrEMBL Database performing an automated protein sequence annotation
- InterPro Integration of protein domain and protein family databases
References
- Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006). "Pfam: clans, web tools and services". Nucleic Acids Res. 34: D247-D251. PMID 16381856.
- Finn RD, Marshall M, Bateman A (2005). "iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions". Bioinformatics 21: 410-412. PMID 15353450.
- Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004). "The Pfam protein families database". Nucleic Acids Res. 32(Database issue): D138-D141. PMID 14681378.
External links
- Pfam - Protein family database at Sanger Institute UK
- Pfam - Protein family database at Janelia Farm Research Campus USA
- Pfam - Protein family database at Center for Genomics and Bioinformatics Sweden
- iPfam - Interactions of Pfam domains in PDB