Open Access
The Universal Protein Resource (UniProt) in 2010
Rolf Apweiler,Maria Jesus Martin,Claire O'Donovan,Michele Magrane,Yasmin Alam-Faruque,Ricardo Antunes,Daniel Barrell,Benoit Bely,M Bingley,David Binns,Lynette Bower,Paul Browne,WM Chan,E. Dimmer,Ruth Y. Eberhardt,A. Fedotov,Rebecca E. Foulger,John S. Garavelli,Rachael P. Huntley,Julius O.B. Jacobsen,M. Kleen,Kati Laiho,Rasko Leinonen,Duncan Legge,Quan Lin,W Liu,Jie Luo,Sandra Orchard,Samuel Patient,Diego Poggioli,Manuela Pruess,Matthew Corbett,G di Martino,M Donnelly,P van Rensburg,Amos Marc Bairoch,Lydie Bougueleret,Ioannis Xenarios,S Altairac,Andrea H. Auchincloss,Ghislaine Argoud-Puy,Kristian B. Axelsen,Delphine Baratin,M. C. Blatter,Brigitte Boeckmann,Jerven Bolleman,L. Bollondi,Emmanuel Boutet,SB Quintaje,Lionel Breuza,Alan Bridge,E. Decastro,L Ciapina,D Coral,Elisabeth Coudert,Isabelle Cusin,G Delbard,M Doche,Dolnide Dornevil,Paula Duek Roggli,Séverine Duvaud,Anne Estreicher,L Famiglietti,M Feuermann,Sebastien Gehant,N. Farriol-Mathis,Serenella Ferro,Elisabeth Gasteiger,Alain Gateau,Gerritsen,Arnaud Gos,Nadine Gruaz-Gumowski,Ursula Hinz,Chantal Hulo,Nicolas Hulo,J. James,S. Jimenez,Florence Jungo,T. Kappler,Guillaume Keller,Corinne Lachaize,L Lane-Guermonprez,Petra S. Langendijk-Genevaux,Lara,P Lemercier,Damien Lieberherr,Tdo Lima,Mangold,Xavier D. Martin,Patrick Masson,M. Moinat,Anne Morgat,Anaïs Mottaz,Salvo Paesano,Ivo Pedruzzi,Sandrine Pilbout,Pillet,Sylvain Poux,Monica Pozzato,Nicole Redaschi,Catherine Rivoire,Bernd Roechert,Maria Victoria Schneider,Christian J. A. Sigrist,K Sonesson,S Staehli,Eleanor J Stanley,Andre Stutz,Shyamala Sundaram,Michael Tognolli,Laure Verbregue,A-L Veuthey,L Yip,L Zuletta,Cathy H. Wu,Cecilia N. Arighi,Leslie Arminski,Winona C. Barker,Chuming Chen,Yingfei Chen,Z-Z Hu,Hongzhan Huang,Raja Mazumder,Peter B. McGarvey,Darren A. Natale,Jules Nchoutmboube,Natalia V. Petrova,N Subramanian,Baris E. Suzek,U. Ugochukwu,Sona Vasudevan,C. R. Vinayaka,LS Yeh,Jian Zhang +133 more
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The article was published on 2010-01-01 and is currently open access. It has received 961 citations till now. The article focuses on the topics: Universal Protein Resource & UniProt.read more
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HMMER web server: interactive sequence similarity searching
TL;DR: This work has focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.
Journal ArticleDOI
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
Damian Szklarczyk,Andrea Franceschini,Michael Kuhn,Milan Simonovic,Alexander Roth,Pablo Minguez,Tobias Doerks,Manuel Stark,Jean Muller,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: An update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING), which provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information.
Journal ArticleDOI
A new bioinformatics analysis tools framework at EMBL–EBI
Mickael Goujon,Hamish McWilliam,Weizhong Li,Franck Valentin,Silvano Squizzato,Juri Paern,Rodrigo Lopez +6 more
TL;DR: A new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface is presented.
Journal ArticleDOI
SMART 7: recent updates to the protein domain annotation resource
TL;DR: ‘metaSMART’ was introduced as a novel subresource dedicated to the exploration and analysis of domain architectures in various metagenomics data sets, covering the complete annotations for SMART and Pfam domains, as well as the complete set of protein descriptions, allowing users to quickly find relevant information.
Journal ArticleDOI
OPM database and PPM web server: resources for positioning of proteins in membranes
TL;DR: The Orientations of Proteins in Membranes (OPM) database is a curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization.
References
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Journal ArticleDOI
KEGG for linking genomes to life and the environment
Minoru Kanehisa,Michihiro Araki,Susumu Goto,Masahiro Hattori,Mika Hirakawa,Masumi Itoh,Toshiaki Katayama,Shuichi Kawashima,Shujiro Okuda,Toshiaki Tokimatsu,Yoshihiro Yamanishi +10 more
TL;DR: KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps, and the KEGG resource is being expanded to suit the needs for practical applications.
Journal ArticleDOI
STRING 8—a global view on proteins and their functional interactions in 630 organisms
Lars Juhl Jensen,Michael Kuhn,Manuel Stark,Samuel Chaffron,Christopher J. Creevey,Jean Muller,T. Doerks,Philippe Julien,Alexander Roth,Milan Simonovic,Peer Bork,Christian von Mering +11 more
TL;DR: The most important new developments in STRING 8 over previous releases include a URL-based programming interface, improved interaction prediction via genomic neighborhood in prokaryotes, and the inclusion of protein structures.
Journal ArticleDOI
The genome sequence of Schizosaccharomyces pombe
Valerie Wood,R. Gwilliam,Marie-Adèle Rajandream,M. Lyne,Rachel Lyne,A. Stewart,J. Sgouros,N. Peat,Jacqueline Hayles,Stephen Baker,D. Basham,Sharen Bowman,Karen Brooks,D. Brown,Steve D.M. Brown,Tracey Chillingworth,Carol Churcher,Mark O. Collins,R. Connor,Ann Cronin,P. Davis,Theresa Feltwell,Andrew G. Fraser,S. Gentles,Arlette Goble,N. Hamlin,David Harris,J. Hidalgo,Geoffrey M. Hodgson,S. Holroyd,T. Hornsby,S. Howarth,Elizabeth J. Huckle,Sarah E. Hunt,Kay Jagels,Kylie R. James,L. Jones,Matthew Jones,S. Leather,S. McDonald,J. McLean,P. Mooney,Sharon Moule,Karen Mungall,Lee Murphy,D. Niblett,C. Odell,Karen Oliver,Susan O'Neil,D. Pearson,Michael A. Quail,Ester Rabbinowitsch,Kim Rutherford,Simon Rutter,David L. Saunders,Kathy Seeger,Sarah Sharp,Jason Skelton,Mark Simmonds,R. Squares,S. Squares,K. Stevens,K. Taylor,Ruth Taylor,Adrian Tivey,S. Walsh,T. Warren,S. Whitehead,John Woodward,Guido Volckaert,Rita Aert,Johan Robben,B. Grymonprez,I. Weltjens,E. Vanstreels,Michael A. Rieger,M. Schafer,S. Muller-Auer,C. Gabel,M. Fuchs,C. Fritzc,E. Holzer,D. Moestl,H. Hilbert,K. Borzym,I. Langer,Alfred Beck,Hans Lehrach,Richard Reinhardt,Thomas M. Pohl,P. Eger,Wolfgang Zimmermann,H. Wedler,R. Wambutt,Bénédicte Purnelle,André Goffeau,Edouard Cadieu,Stéphane Dréano,Stéphanie Gloux,Valerie Lelaure,Stéphanie Mottier,Francis Galibert,Stephen J. Aves,Z. Xiang,Cherryl Hunt,Karen Moore,S. M. Hurst,M. Lucas,M. Rochet,Claude Gaillardin,Victor A. Tallada,Victor A. Tallada,Andrés Garzón,Andrés Garzón,G. Thode,Rafael R. Daga,Rafael R. Daga,L. Cruzado,Juan Jimenez,Juan Jimenez,Miguel del Nogal Sánchez,F. del Rey,J. Benito,Angel Domínguez,José L. Revuelta,Sergio Moreno,John Armstrong,Susan L. Forsburg,L. Cerrutti,Todd M. Lowe,W. R. McCombie,Ian T. Paulsen,Judith A. Potashkin,G. V. Shpakovski,David W. Ussery,Bart Barrell,Paul Nurse +136 more
TL;DR: The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote, is sequenced and highly conserved genes important for eukARYotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing are identified.
Journal ArticleDOI
UniRef: comprehensive and non-redundant UniProt reference clusters.
TL;DR: The UniRef (UniProt Reference Clusters) provides clustered sets of sequences from the UniProt Knowledgebase and selected UniProt Archive records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences.
Journal ArticleDOI
The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
David Swarbreck,Christopher Wilks,Philippe Lamesch,Tanya Z. Berardini,Margarita Garcia-Hernandez,Hartmut Foerster,Donghui Li,Tom Meyer,Robert J. Muller,Larry Ploetz,Amie Radenbaugh,Shanker Singh,Vanessa Swing,Christophe Tissier,Peifen Zhang,Eva Huala +15 more
TL;DR: A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models).
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more