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1. InterPro, progress and status in 2005.

Author

Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan 0001, and Cathy H. Wu

Published
2005
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3. The InterPro Database, 2003 brings increased coverage and new features

Author

Emmanuel Courcelle, Teresa K. Attwood, Evgeny M. Zdobnov, Nicolas Hulo, Sandra Orchard, Chris P. Ponting, Margaret Biswas, Sam Griffiths-Jones, Paul Bradley, Ivica Letunic, Robert M. Vaughan, David M. Lonsdale, Richard R. Copley, Marco Pagni, Rodrigo Lopez, Daniel H. Haft, Peer Bork, Jeremy D. Selengut, Nicola Mulder, Ujjwal Das, Wolfgang Fleischmann, Richard Durbin, Laurent Falquet, Rolf Apweiler, Phillip Bucher, Florence Servant, Ville Silventoinen, Alexander Kanapin, Alex Bateman, David Peyruc, Nicola Harte, Christian J. A. Sigrist, Daniel Barrell, Amos Marc Bairoch, Daniel Kahn, David Binns, Maria Krestyaninova, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Bairoch, Amos Marc, Falquet, Laurent, Hulo, Nicolas, Zdobnov, Evgeny, and MDC Library

Subjects
Proteins/chemistry/genetics/metabolism, Repetitive Sequences, Amino Acid, 0106 biological sciences, InterPro, Protein Structure, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Web server, 570 Life Sciences, PROSITE, Biology, computer.software_genre, 01 natural sciences, Repetitive Sequences, 610 Medical Sciences, Medicine, Databases, User-Computer Interface, 03 medical and health sciences, TIGRFAMs, Computer Graphics, Genetics, Animals, Protein Databases, ddc:576, Tertiary Protein Structure, Databases, Protein, Protein Processing, 030304 developmental biology, 0303 health sciences, Database, Protein, Post-Translational, Proteins, Articles, Protein Structure, Tertiary, Amino Acid, Post translational, Cardiovascular and Metabolic Diseases, Amino Acid Repetitive Sequences, Protein processing, Protein signature, Protein Processing, Post-Translational, computer, Tertiary, Post-Translational Protein Processing, Autre (Sciences du Vivant), 010606 plant biology & botany
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).

Published
2003
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4. InterPro, progress and status in 2005

Author

Ivica Letunic, Jeremy D. Selengut, Paul Bradley, Alex L. Mitchell, Ujjwal Das, David Binns, Julian Gough, John Maslen, Teresa K. Attwood, Robert M. Vaughan, Cathy H. Wu, Christian J. A. Sigrist, David J. Studholme, Anastasia N. Nikolskaya, Rodrigo Lopez, Martin Madera, Emmanuel Courcelle, Daniel H. Haft, Nicola Harte, Alexander Kanapin, Marco Pagni, Maria Krestyaninova, Rolf Apweiler, Nicolas Hulo, Richard R. Copley, Sandra Orchard, David M. Lonsdale, Chris P. Ponting, Alex Bateman, Lorenzo Cerutti, Amos Marc Bairoch, Daniel Kahn, Richard Durbin, Phillip Bucher, Peer Bork, Jennifer McDowall, Nicola Mulder, Wolfgang Fleischmann, Emmanuel Quevillon, Ville Silventoinen, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and MDC Library

Subjects
InterPro, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Architecture domain, Protein family, Simple Modular Architecture Research Tool, Protein Sequence Analysis, Databases, Protein/trends, 570 Life Sciences, Computational biology, PROSITE, Biology, Bioinformatics, 610 Medical Sciences, Medicine, 03 medical and health sciences, Annotation, TIGRFAMs, Sequence Analysis, Protein, Genetics, Humans, Protein Databases, ddc:576, Tertiary Protein Structure, Databases, Protein, 030304 developmental biology, Proteins/chemistry/classification, 0303 health sciences, 030302 biochemistry & molecular biology, Proteins, Articles, Protein Structure, Tertiary, Systems Integration, Cardiovascular and Metabolic Diseases, UniProt, Sequence Alignment, Autre (Sciences du Vivant)
Abstract

International audience; InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Published
2005
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5. Occurrence of oligopurine.oligopyrimidine tracts in eukaryotic and prokaryotic genes

Author

Gad Yagil and Phillip Bucher

Subjects
Chloroplasts, Molecular Sequence Data, Biology, Biochemistry, Genome, Endocrinology, Plasmid, Intergenic region, Yeasts, Tobacco, Genetics, Escherichia coli, Coding region, Molecular Biology, Gene, Purine Nucleotides, Regulator gene, Base Composition, Base Sequence, Intron, DNA, Plants, Toxic, Eukaryotic Cells, Prokaryotic Cells, Regulatory sequence, Viruses, Pyrimidine Nucleotides
Abstract

A program to analyse the length and frequency distribution of specific base tracts in genomic sequences is described. The frequency of oligopurine.oligopyrimidine tracts (R.Y. tracts) in a data base of 163 transcribed genes is analysed and compared. The complete genomes of SV40 virus, N. tobacum chloroplast, yeast 2 micron plasmid, bacteriophage lambda, plasmid pBR322 and the E. coli lac operon are also analyzed. A highly significant overrepresentation of oligopurine and oligopyrimidine tracts is observed in all eukaryotic genes examined, as well as in the chloroplast genome. The overrepresentation is evident in all gene subregions of the chloroplast, in the following order: intergenic regions, 3' downstream and 5' upstream (promoter), 5' and 3' untranslated, introns and coding regions. In genes coding for basic proteins, oligopurine rather than oligopyrimidine tracts are found on the coding stand. In prokaryotic genes only the longest R.Y. tracts (greater than or equal to 12) are found in excess, and are concentrated near regulatory regions. While a structural role for R.Y. tracts is most likely in intergenic regions, a functional role, as initiation sites for strand separation, is proposed for regulatory gene regions.

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