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Nucleic Acids Research, 2003, Vol. 31, No. 1 315-318
© 2003 Oxford University Press

The InterPro Database, 2003 brings increased coverage and new features

Nicola J. Mulder*,1, Rolf Apweiler1, Teresa K. Attwood3, Amos Bairoch4, Daniel Barrell1, Alex Bateman2, David Binns1, Margaret Biswas5, Paul Bradley1,3, Peer Bork6, Phillip Bucher7, Richard R. Copley8, Emmanuel Courcelle9, Ujjwal Das1, Richard Durbin2, Laurent Falquet7, Wolfgang Fleischmann1, Sam Griffiths-Jones2, Daniel Haft10, Nicola Harte1, Nicolas Hulo4, Daniel Kahn9, Alexander Kanapin1, Maria Krestyaninova1, Rodrigo Lopez1, Ivica Letunic6, David Lonsdale1, Ville Silventoinen1, Sandra E. Orchard1, Marco Pagni7, David Peyruc9, Chris P. Ponting11, Jeremy D. Selengut10, Florence Servant1, Christian J. A. Sigrist4, Robert Vaughan1 and Evgueni M. Zdobnov6,12

1 EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK 2 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK 3 School of Biological Sciences and Department of Computer Science, The University of Manchester, Manchester, UK 4 Swiss Institute for Bioinformatics, Geneva, Switzerland 5 ViaLactia Biosciences, Newmarket Auckland, New Zealand 6 Biocomputing Unit EMBL, Heidelberg, Germany 7 Swiss Institute for Experimental Cancer Research, Lausanne, Switzerland 8 Wellcome Trust Centre for Human Genetics, Oxford, UK 9 CNRS/INRA, Toulouse, France 10 The Institute for Genomic Research, MD, USA 11 MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, UK 12 EMBL, Heidelberg, Germany

*To whom correspondence should be addressed. Tel: +44 1223 494602; Fax: +44 1223 494468; Email: mulder{at}ebi.ac.uk

ABSTRACT

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).


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 Proc. Natl. Acad. Sci. USAHome page
E. Kolker, A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, X. Qiu, K. J. Auberry, et al.
Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations
PNAS, February 8, 2005; 102(6): 2099 - 2104.
[Abstract] [Full Text] [PDF]

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 DNA ResHome page
K. Iida, M. Seki, T. Sakurai, M. Satou, K. Akiyama, T. Toyoda, A. Konagaya, and K. Shinozaki
RARTF: Database and Tools for Complete Sets of Arabidopsis Transcription Factors.
DNA Res, January 1, 2005; 12(4): 247 - 256.
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 Nucleic Acids ResHome page
C. Kanz, P. Aldebert, N. Althorpe, W. Baker, A. Baldwin, K. Bates, P. Browne, A. van den Broek, M. Castro, G. Cochrane, et al.
The EMBL Nucleotide Sequence Database
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D29 - D33.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
C. Brooksbank, G. Cameron, and J. Thornton
The European Bioinformatics Institute's data resources: towards systems biology
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D46 - D53.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
P. Kim, N. Kim, Y. Lee, B. Kim, Y. Shin, and S. Lee
ECgene: genome annotation for alternative splicing
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D75 - D79.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
H.-D. Huang, J.-T. Horng, F.-M. Lin, Y.-C. Chang, and C.-C. Huang
SpliceInfo: an information repository for mRNA alternative splicing in human genome
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D80 - D85.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
S. J. Hubbard, D. V. Grafham, K. J. Beattie, I. M. Overton, S. R. McLaren, M. D.R. Croning, P. E. Boardman, J. K. Bonfield, J. Burnside, R. M. Davies, et al.
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
Genome Res., January 1, 2005; 15(1): 174 - 183.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
F. Mignone, G. Grillo, F. Licciulli, M. Iacono, S. Liuni, P. J. Kersey, J. Duarte, C. Saccone, and G. Pesole
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D141 - D146.
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 Nucleic Acids ResHome page
A. Bairoch, R. Apweiler, C. H. Wu, W. C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, et al.
The Universal Protein Resource (UniProt)
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D154 - D159.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
Q. J. Su, L. Lu, S. Saxonov, and D. L. Brutlag
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D178 - D182.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
A. Heger, C. A. Wilton, A. Sivakumar, and L. Holm
ADDA: a domain database with global coverage of the protein universe
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D188 - D191.
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 Nucleic Acids ResHome page
S. Abhiman and E. L. L. Sonnhammer
FunShift: a database of function shift analysis on protein subfamilies
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D197 - D200.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
C. Bru, E. Courcelle, S. Carrere, Y. Beausse, S. Dalmar, and D. Kahn
The ProDom database of protein domain families: more emphasis on 3D
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D212 - D215.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
N. Kaplan, O. Sasson, U. Inbar, M. Friedlich, M. Fromer, H. Fleischer, E. Portugaly, N. Linial, and M. Linial
ProtoNet 4.0: A hierarchical classification of one million protein sequences
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D216 - D218.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
K. Vlahovicek, L. Kajan, V. Agoston, and S. Pongor
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D223 - D225.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
T. Meinel, A. Krause, H. Luz, M. Vingron, and E. Staub
The SYSTERS Protein Family Database in 2005
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D226 - D229.
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 Nucleic Acids ResHome page
S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, D. Barrell, R. Apweiler, and K. Henrick
E-MSD: an integrated data resource for bioinformatics
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D262 - D265.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
H. Mi, B. Lazareva-Ulitsky, R. Loo, A. Kejariwal, J. Vandergriff, S. Rabkin, N. Guo, A. Muruganujan, O. Doremieux, M. J. Campbell, et al.
The PANTHER database of protein families, subfamilies, functions and pathways
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D284 - D288.
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 Nucleic Acids ResHome page
P. Kersey, L. Bower, L. Morris, A. Horne, R. Petryszak, C. Kanz, A. Kanapin, U. Das, K. Michoud, I. Phan, et al.
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D297 - D302.
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 Nucleic Acids ResHome page
P. Stothard, G. Van Domselaar, S. Shrivastava, A. Guo, B. O'Neill, J. Cruz, M. Ellison, and D. S. Wishart
BacMap: an interactive picture atlas of annotated bacterial genomes
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D317 - D320.
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 Nucleic Acids ResHome page
J. Wang, Q. Xia, X. He, M. Dai, J. Ruan, J. Chen, G. Yu, H. Yuan, Y. Hu, R. Li, et al.
SilkDB: a knowledgebase for silkworm biology and genomics
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D399 - D402.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
J. Wang, X. He, J. Ruan, M. Dai, J. Chen, Y. Zhang, Y. Hu, C. Ye, S. Li, L. Cong, et al.
ChickVD: a sequence variation database for the chicken genome
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D438 - D441.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, et al.
Ensembl 2005
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D447 - D453.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
H. Parkinson, U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. Garcia Lara, E. Holloway, M. Kapushesky, et al.
ArrayExpress--a public repository for microarray gene expression data at the EBI
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D553 - D555.
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 Nucleic Acids ResHome page
S. Rudd
openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D622 - D627.
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 Nucleic Acids ResHome page
Y. Ito, K. Arikawa, B. A. Antonio, I. Ohta, S. Naito, Y. Mukai, A. Shimano, M. Masukawa, M. Shibata, M. Yamamoto, et al.
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D651 - D655.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
M. D. Gonzales, E. Archuleta, A. Farmer, K. Gajendran, D. Grant, R. Shoemaker, W. D. Beavis, and M. E. Waugh
The Legume Information System (LIS): an integrated information resource for comparative legume biology
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D660 - D665.
[Abstract] [Full Text] [PDF]

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 Learn. Mem.Home page
M. Pinter, D. D. Lent, and N. J. Strausfeld
Memory consolidation and gene expression in Periplaneta americana
Learn. Mem., January 1, 2005; 12(1): 30 - 38.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
K. Galani, T. A. Nissan, E. Petfalski, D. Tollervey, and E. Hurt
Rea1, a Dynein-related Nuclear AAA-ATPase, Is Involved in Late rRNA Processing and Nuclear Export of 60 S Subunits
J. Biol. Chem., December 31, 2004; 279(53): 55411 - 55418.
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 Plant Cell PhysiolHome page
K. Mashiguchi, I. Yamaguchi, and Y. Suzuki
Isolation and Identification of Glycosylphosphatidylinositol-Anchored Arabinogalactan Proteins and Novel {beta}-Glucosyl Yariv-Reactive Proteins from Seeds of Rice (Oryza sativa)
Plant Cell Physiol., December 15, 2004; 45(12): 1817 - 1829.
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 Plant Physiol.Home page
M. Sauter, K. A. Cornell, S. Beszteri, and G. Rzewuski
Functional Analysis of Methylthioribose Kinase Genes in Plants
Plant Physiology, December 1, 2004; 136(4): 4061 - 4071.
[Abstract] [Full Text] [PDF]

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 J. Biol. Chem.Home page
J. J. McElwee, E. Schuster, E. Blanc, J. H. Thomas, and D. Gems
Shared Transcriptional Signature in Caenorhabditis elegans Dauer Larvae and Long-lived daf-2 Mutants Implicates Detoxification System in Longevity Assurance
J. Biol. Chem., October 22, 2004; 279(43): 44533 - 44543.
[Abstract] [Full Text] [PDF]


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