Nucleic Acids Research, Vol 26, Issue 1 320-322, Copyright © 1998 by Oxford University Press
EL Sonnhammer, SR Eddy, E Birney, A Bateman and R Durbin
Pfam contains multiple alignments and hidden Markov model based profiles
(HMM-profiles) of complete protein domains. The definition of domain
boundaries, family members and alignment is done semi- automatically based
on expert knowledge, sequence similarity, other protein family databases
and the ability of HMM-profiles to correctly identify and align the
members. Release 2.0 of Pfam contains 527 manually verified families which
are available for browsing and on-line searching via the World Wide Web in
the UK at http://www.sanger.ac.uk/Pfam/ and in the US at
http://genome.wustl. edu/Pfam/ Pfam 2.0 matches one or more domains in 50%
of Swissprot-34 sequences, and 25% of a large sample of predicted proteins
from the Caenorhabditis elegans genome.
ARTICLES
Pfam: multiple sequence alignments and HMM-profiles of protein domains
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Building 38A, Room 8N805, National Institutes of Health, Bethesda, MD 20894, USA. sonnhammer@ncbi.nlm.nih.gov
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C. L. Afonso, E. R. Tulman, Z. Lu, C. A. Balinsky, B. A. Moser, J. J. Becnel, D. L. Rock, and G. F. Kutish Genome Sequence of a Baculovirus Pathogenic for Culex nigripalpus J. Virol., November 15, 2001; 75(22): 11157 - 11165. [Abstract] [Full Text] [PDF]
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P. Vaccaro, B. Brannetti, L. Montecchi-Palazzi, S. Philipp, M. H. Citterich, G. Cesareni, and L. Dente Distinct Binding Specificity of the Multiple PDZ Domains of INADL, a Human Protein with Homology to INAD from Drosophila melanogaster J. Biol. Chem., November 2, 2001; 276(45): 42122 - 42130. [Abstract] [Full Text] [PDF]
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Y. Pouliot, J. Gao, Q. J. Su, G. G. Liu, and X. B. Ling DIAN: A Novel Algorithm for Genome Ontological Classification Genome Res., October 1, 2001; 11(10): 1766 - 1779. [Abstract] [Full Text] [PDF]
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P. J. Fernandes, J. A. C. Powell, and J. A. C. Archer Construction of Rhodococcus random mutagenesis libraries using Tn5 transposition complexes Microbiology, September 1, 2001; 147(9): 2529 - 2536. [Abstract] [Full Text] [PDF]
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S.-H. Shiu and A. B. Bleecker Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases PNAS, August 23, 2001; (2001) 181141598. [Abstract] [Full Text] [PDF]
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J. Murvai, K. Vlahovicek, C. Szepesvari, and S. Pongor Prediction of Protein Functional Domains from Sequences Using Artificial Neural Networks Genome Res., August 1, 2001; 11(8): 1410 - 1417. [Abstract] [Full Text] [PDF]
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I. Chen and E. C. Gotschlich ComE, a Competence Protein from Neisseria gonorrhoeae with DNA-Binding Activity J. Bacteriol., May 15, 2001; 183(10): 3160 - 3168. [Abstract] [Full Text]
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I. Chambaud, R. Heilig, S. Ferris, V. Barbe, D. Samson, F. Galisson, I. Moszer, K. Dybvig, H. Wroblewski, A. Viari, et al. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis Nucleic Acids Res., May 15, 2001; 29(10): 2145 - 2153. [Abstract] [Full Text] [PDF]
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H. Yang, I. T. Phan, S. Fitz-Gibbon, M. K. K. Shivji, R. D. Wood, W. M. Clendenin, E. C. Hyman, and J. H. Miller A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum Nucleic Acids Res., February 1, 2001; 29(3): 604 - 613. [Abstract] [Full Text] [PDF]
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C. L. Afonso, E. R. Tulman, Z. Lu, L. Zsak, D. L. Rock, and G. F. Kutish The Genome of Turkey Herpesvirus J. Virol., January 15, 2001; 75(2): 971 - 978. [Abstract] [Full Text]
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R. J. M. Bongaerts, H.-P. Heinz, U. Hadding, and G. Zysk Antigenicity, Expression, and Molecular Characterization of Surface-Located Pullulanase of Streptococcus pneumoniae Infect. Immun., December 1, 2000; 68(12): 7141 - 7143. [Abstract] [Full Text] [PDF]
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C. G. Friedrich, A. Quentmeier, F. Bardischewsky, D. Rother, R. Kraft, S. Kostka, and H. Prinz Novel Genes Coding for Lithotrophic Sulfur Oxidation of Paracoccus pantotrophus GB17 J. Bacteriol., September 1, 2000; 182(17): 4677 - 4687. [Abstract] [Full Text]
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M. G. Reese, G. Hartzell, N. L. Harris, U. Ohler, J. F. Abril, and S. E. Lewis Genome Annotation Assessment in Drosophila melanogaster Genome Res., April 1, 2000; 10(4): 483 - 501. [Abstract] [Full Text]
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H. Yang, M. M. Slupska, Y.-F. Wei, J. H. Tai, W. M. Luther, Y.-R. Xia, D. M. Shih, J.-H. Chiang, C. Baikalov, S. Fitz-Gibbon, et al. Cloning and Characterization of a New Member of the Nudix Hydrolases from Human and Mouse J. Biol. Chem., March 17, 2000; 275(12): 8844 - 8853. [Abstract] [Full Text] [PDF]
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G. Subramanian, E. V. Koonin, and L. Aravind Comparative Genome Analysis of the Pathogenic Spirochetes Borrelia burgdorferi and Treponema pallidum Infect. Immun., March 1, 2000; 68(3): 1633 - 1648. [Abstract] [Full Text] [PDF]
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H. Hutter, B. E. Vogel, J. D. Plenefisch, C. R. Norris, R. B. Proenca, J. Spieth, C. Guo, S. Mastwal, X. Zhu, I. S. A. J. Scheel, et al. Conservation and Novelty in the Evolution of Cell Adhesion and Extracellular Matrix Genes Science, February 11, 2000; 287(5455): 989 - 994. [Abstract] [Full Text]
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B. D. Lindenbach and C. M. Rice Genetic Interaction of Flavivirus Nonstructural Proteins NS1 and NS4A as a Determinant of Replicase Function J. Virol., June 1, 1999; 73(6): 4611 - 4621. [Abstract] [Full Text]
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The C. elegans Sequencing Consortium Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology Science, December 11, 1998; 282(5396): 2012 - 2018. [Abstract] [Full Text]
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