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      Pfam: clans, web tools and services

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          Abstract

          Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK ( http://www.sanger.ac.uk/Software/Pfam/), the USA ( http://pfam.wustl.edu/), France ( http://pfam.jouy.inra.fr/) and Sweden ( http://pfam.cgb.ki.se/).

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          The Pfam protein families database.

          A. Bateman, Lachlan Coin (2004)
          Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).
          Article 0 comments Cited 1100 times – based on 0 reviews     Review now
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            SMART 4.0: towards genomic data integration.

            Ivica Letunic, Richard Copley, Steffen Schmidt … (2004)
            SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins. The January 2004 release of SMART contains 685 protein domains. New developments in SMART are centred on the integration of data from completed metazoan genomes. SMART now uses predicted proteins from complete genomes in its source sequence databases, and integrates these with predictions of orthology. New visualization tools have been developed to allow analysis of gene intron-exon structure within the context of protein domain structure, and to align these displays to provide schematic comparisons of orthologous genes, or multiple transcripts from the same gene. Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries.
            Article 0 comments Cited 268 times – based on 0 reviews     Review now
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              SCOP database in 2004: refinements integrate structure and sequence family data.

              Antonina Andreeva, Dave Howorth, Steven Brenner … (2004)
              The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
              Article 0 comments Cited 231 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): Nucleic Acids Research
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: 01 January 2006
                Publication date (Print): 01 January 2006
                Publication date (Electronic): 28 December 2005
                Volume: 34
                Issue: Database issue
                Pages: D247-D251
                Affiliations
                Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK
                1Center for Genomics and Bioinformatics, Karolinska Institutet S-171 77 Stockholm, Sweden
                2Department of Genetics, Howard Hughes Medical Institute, Washington University School of Medicine St Louis, MO 63110, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +44 1223 495330; Fax: +44 1223 494919; Email: rdf@ 123456sanger.ac.uk
                Article
                DOI: 10.1093/nar/gkj149
                PMC ID: 1347511
                PubMed ID: 16381856
                SO-VID: fb9eb305-3060-4b8c-8ab1-7ff50522085e
                Copyright © © The Author 2006. Published by Oxford University Press. All rights reserved
                License:

                The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@ 123456oxfordjournals.org

                History
                Date received : 15 September 2005
                Date revision received : 19 October 2005
                Date accepted : 28 October 2005
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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