Nucleic Acids Research, 2001, Vol. 29, No. 1 37-40
© 2001 Oxford University Press
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
1EMBL Outstation – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 2School of Biological Sciences, The University of Manchester, Manchester, UK, 3Swiss Institute for Bioinformatics, Geneva, Switzerland, 4The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 5Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland, 6CNRS/INRA, Toulouse, France and 7Department of Informatics, University of Bergen, HIB, Bergen, Norway
Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1 000 000 hits from 462 500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp{at}ebi.ac.uk.
* To whom correspondence should be addressed. Tel: +44 1223 494 435; Fax: +44 1223 494 468; Email: rolf.apweiler{at}ebi.ac.uk
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D. P. Hill, D. A. Begley, J. H. Finger, T. F. Hayamizu, I. J. McCright, C. M. Smith, J. S. Beal, L. E. Corbani, J. A. Blake, J. T. Eppig, et al. The mouse Gene Expression Database (GXD): updates and enhancements Nucleic Acids Res., January 1, 2004; 32(90001): D568 - 571. [Abstract] [Full Text] [PDF]
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Y. Mudgil, S.-H. Shiu, S. L. Stone, J. N. Salt, and D. R. Goring A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family Plant Physiology, January 1, 2004; 134(1): 59 - 66. [Abstract] [Full Text] [PDF]
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A. J. Poustka, D. Groth, S. Hennig, S. Thamm, A. Cameron, A. Beck, R. Reinhardt, R. Herwig, G. Panopoulou, and H. Lehrach Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters Genome Res., December 1, 2003; 13(12): 2736 - 2746. [Abstract] [Full Text] [PDF]
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E. Waters, M. J. Hohn, I. Ahel, D. E. Graham, M. D. Adams, M. Barnstead, K. Y. Beeson, L. Bibbs, R. Bolanos, M. Keller, et al. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism PNAS, October 28, 2003; 100(22): 12984 - 12988. [Abstract] [Full Text] [PDF]
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D. Rathore, S. C. L. Hrstka, J. B. Sacci Jr., P. De la Vega, R. J. Linhardt, S. Kumar, and T. F. McCutchan Molecular Mechanism of Host Specificity in Plasmodium falciparum Infection: ROLE OF CIRCUMSPOROZOITE PROTEIN J. Biol. Chem., October 17, 2003; 278(42): 40905 - 40910. [Abstract] [Full Text] [PDF]
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N. Hall, M. Berriman, N. J. Lennard, B. R. Harris, C. Hertz-Fowler, E. N. Bart-Delabesse, C. S. Gerrard, R. J. Atkin, A. J. Barron, S. Bowman, et al. The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism Nucleic Acids Res., August 15, 2003; 31(16): 4864 - 4873. [Abstract] [Full Text] [PDF]
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S. N. M. Reid, C. Yamashita, and D. B. Farber Retinoschisin, a Photoreceptor-Secreted Protein, and Its Interaction with Bipolar and Muller Cells J. Neurosci., July 9, 2003; 23(14): 6030 - 6040. [Abstract] [Full Text] [PDF]
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R. Chattopadhyay, D. Rathore, H. Fujioka, S. Kumar, P. de la Vega, D. Haynes, K. Moch, D. Fryauff, R. Wang, D. J. Carucci, et al. PfSPATR, a Plasmodium falciparum Protein Containing an Altered Thrombospondin Type I Repeat Domain Is Expressed at Several Stages of the Parasite Life Cycle and Is the Target of Inhibitory Antibodies J. Biol. Chem., July 3, 2003; 278(28): 25977 - 25981. [Abstract] [Full Text] [PDF]
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P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, M. Mattingsdal, S. Cameron, D. M. A. Martin, G. Ausiello, B. Brannetti, A. Costantini, et al. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins Nucleic Acids Res., July 1, 2003; 31(13): 3625 - 3630. [Abstract] [Full Text] [PDF]
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T. A. Torto, S. Li, A. Styer, E. Huitema, A. Testa, N. A.R. Gow, P. van West, and S. Kamoun EST Mining and Functional Expression Assays Identify Extracellular Effector Proteins From the Plant Pathogen Phytophthora Genome Res., July 1, 2003; 13(7): 1675 - 1685. [Abstract] [Full Text] [PDF]
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T. Nishiyama, T. Fujita, T. Shin-I, M. Seki, H. Nishide, I. Uchiyama, A. Kamiya, P. Carninci, Y. Hayashizaki, K. Shinozaki, et al. Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolution PNAS, June 24, 2003; 100(13): 8007 - 8012. [Abstract] [Full Text] [PDF]
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G. Panopoulou, S. Hennig, D. Groth, A. Krause, A. J. Poustka, R. Herwig, M. Vingron, and H. Lehrach New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes Genome Res., June 1, 2003; 13(6): 1056 - 1066. [Abstract] [Full Text] [PDF]
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V. Brusic, R. S. Pillai, D. G. Silva, N. Petrovsky, RIKEN GER Group, GSL Members, and C. Schonbach Cytokine-Related Genes Identified From the RIKEN Full-Length Mouse cDNA Data Set Genome Res., June 1, 2003; 13(6): 1307 - 1317. [Abstract] [Full Text] [PDF]
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