HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147 USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK, Institute of Biotechnology and Department of Biological and Environmental Sciences, University of Helsinki, PO Box 56 (Viikinkaari 5), 00014 Helsinki, Finland and Stockholm Bioinformatics Center, Swedish eScience Research Center, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, PO Box 1031, SE-17121 Solna, Sweden.
Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30. doi: 10.1093/nar/gkt1223. Epub 2013 Nov 27.
Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures.
Pfam 可通过英国服务器（http://pfam.sanger.ac.uk/）和美国服务器（http://pfam.janelia.org/）访问，是一个广泛使用的蛋白质家族数据库，在当前版本 27.0 中包含 14831 个手动整理的条目。自 2 年前的上一次更新文章以来，我们生成了 1182 个新家族，并保持了 UniProt 知识库（UniProtKB）序列覆盖度接近 80%，尽管基础序列数据库的大小增加了 50%。自我们 2012 年描述 Pfam 的文章以来，我们还对 Pfam 提供的基本家族数据之外的功能进行了全面审查。对于每个功能，我们确定了相关性、计算负担、使用统计数据以及在网站上下文中的功能。由于这次审查，我们已经删除了一些功能，增强了其他功能，并开发了新的功能来满足计算生物学不断变化的需求。在这里，我们描述了 Pfam 内容的变化。值得注意的是，我们现在提供了基于四个不同代表性蛋白质组序列数据集的家族比对，以及新的交互式 DNA 搜索界面。我们还讨论了 Pfam 与已知 3D 结构之间的映射关系。
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