Changes

<font face="바탕" size="2">Pfam은 [[ProDom]]에서 진화한 것으로 개념적으로 [[PROSITE]] profile들과 연관된 [[HMM]]들의 집합이다<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>&nbsp;<br /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>Pfam 모델들은&nbsp;유사 단백질의 multiple alignment로 부터</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). &nbspquot;Pfam: clans, web tools and services&quot;추출된 HMM profile이다.<br em>Nucleic Acids Res.</em> <strong>34</strong>: D247-D251. PMID 16381856.</cite>HMMER package로 만들어 지며,<span class="Z3988" title="ctx_ver=Z39.88-2004&nbspamp;HMM의 hmmpfam 명령을 통해,rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&nbspamp;단백질 서열에서rft.genre=article&nbspamp;rft.atitle=Pfam profile의 존재유무를 검사할 수 있다%3A+clans%2C+web+tools+and+services&amp;rft.jtitle=Nucleic+Acids+Res.&amp;rft.date=2006&amp;rft.volume=34&amp;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&amp;rft.pages=D247-D251">&nbsp;</span> <br /li><br /ul>Pfam은 두가지 형태의 profile file을 제공하는데<ul> <li><cite style="FONT-STYLE: normal">Finn RD, Pfam_ls는 완전한 도메인의 구조를 찾을 때 쓰이며Marshall M, Pfam_fs는 부분적인 Bateman A (불완전한2005) 도메인 조각을 찾을 때 쓰인다.&quot;iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions&quot;. <em>Bioinformatics</em> <strong>21</strong>: 410-412. PMID 15353450.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=iPfam%3A+visualization+of+protein-protein+interactions+in+PDB+at+domain+and+amino+acid+resolutions&amp;rft.jtitle=Bioinformatics&amp;rft.date=2005&amp;rft.volume=21&amp;rft.au=Finn+RD%2C+Marshall+M%2C+Bateman+A&amp;rft.pages=410-412">&nbsp;</span> <br /li><br /ul>현재의 버전은 Pfam20으로 8296개의 모델들을 포함하고 있다<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). &quot;The Pfam protein families database&quot;. <em>Nucleic Acids Res.<br /em> <strong>32(Database issue)</strong>: D138-D141. PMID 14681378.<br /cite>PROSITE와는 대조적으로 <span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=The+Pfam entry들은 semi+protein+families+database&amp;rft.jtitle=Nucleic+Acids+Res.&amp;rft.date=2004&amp;rft.volume=32%28Database+issue%29&amp;rft.au=Bateman+A%2C+Coin+L%2C+Durbin+R%2C+Finn+RD%2C+Hollich+V%2C+Griffiths-automatic하게 생성되어 비교적 쉽게 update 된다Jones+S%2C+Khanna+A%2C+Marshall+M%2C+Moxon+S%2C+Sonnhammer+EL%2C+Studholme+DJ%2C+Yeats+C%2C+Eddy+SR&amp;rft.pages=D138-D141">&nbsp;</span> </li><br /ul><p>Pfam의 초기버젼에서는 비교적 낮은 정밀도를 보여주었지만,&nbsp;밝혀진 서열의 종류가 늘어남에 따라 정확도가 높아지고 있다.<br /p><h2><br span class="mw-headline">External links</span>풍부한 정보를 제공하는 PfamA는 약 74%의 sequence coverage를 나타내며<br /h2><ul> <li>완전히 자동적으로 생성되는 PfamB는 11%의 sequence coverage를 갖는다.Pfam - Protein family database at Sanger Institute UK <br /li>PfmaB로부터는 정보를 얻기가 힘들기는 하지만, 새로운 서열이 추가되면 PfamA로 전환될 것들이다. <li>Pfam - Protein family database at Janelia Farm Research Campus USA <br /li> <li>Pfam - Protein family database at Center for Genomics and Bioinformatics Sweden <br /li>따라서 궁극적으로 85%이상의 단백질에 <li>iPfam - Interactions of Pfam domain을 부여할 수 있다.domains in PDB </li></ul><div class="boilerplate metadata" id="stub"></div><p><br clear="all" /></p></font>