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      TreeFam: a curated database of phylogenetic trees of animal gene families

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          Abstract

          TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; ∼40–85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn.

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          Most cited references35

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          Profile hidden Markov models.

          S. Eddy (1998)
          The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.
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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/).
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              Amino acid substitution matrices from protein blocks.

              S Henikoff, J. Henikoff (1992)
              Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
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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: D572-D580
                Affiliations
                1Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute Beijing 101300, China
                2Institute of Theoretical Physics, Chinese Academy of Sciences Beijing 100080, China
                3Institute of Human Genetics, University of Aarhus DK-8000 Aarhus C, Denmark
                4Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
                5Department of Biochemistry and Molecular Biology, University of Southern Denmark DK-5230 Odense M, Denmark
                6Institute of Computing Technology, Chinese Academy of Sciences Beijing 100080, China
                7University of Washington Genome Center, Department of Medicine, University of Washington Seattle, WA 98195, USA
                8Evolutionary Genomics Department, Department of Energy Joint Genome Institute and Lawrence Berkeley National Laboratory Walnut Creek, California, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +44 1223 834244; Fax: +44 1223 494919; Email: rd@ 123456sanger.ac.uk

                Correspondence may also be addressed to Jun Wang. Tel: +86 10 80481664; Fax: +86 10 80498676; Email: wangj@ 123456genomics.org.cn

                The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors

                Article
                DOI: 10.1093/nar/gkj118
                PMC ID: 1347480
                PubMed ID: 16381935
                SO-VID: b9f2a095-68ae-45d1-a341-491a3f821382
                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 August 2005
                Date revision received : 19 October 2005
                Date accepted : 19 October 2005
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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