Literature DB >> 16204122

Adding some SPICE to DAS.

Andreas Prlić1, Thomas A Down, Tim J P Hubbard.   

Abstract

UNLABELLED: The distributed annotation system (DAS) defines a communication protocol used to exchange biological annotations. It is motivated by the idea that annotations should not be provided by single centralized databases but instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is carried out by DAS clients. The original DAS protocol was designed to serve annotation of genomic sequences. We have extended the protocol to be applicable to macromolecular structures. Here we present SPICE, a new DAS client that can be used to visualize protein sequence and structure annotations. AVAILABILITY: http://www.efamily.org.uk/software/dasclients/spice/

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Year:  2005        PMID： 16204122      PMCID： PMC2656757          DOI： 10.1093/bioinformatics/bti1106

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  6 in total

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Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

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Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

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Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  RASMOL: biomolecular graphics for all.

Authors:  R A Sayle; E J Milner-White
Journal:  Trends Biochem Sci       Date:  1995-09       Impact factor: 13.807

5.  Ensembl 2005.

Authors:  T Hubbard; D Andrews; M Caccamo; G Cameron; Y Chen; M Clamp; L Clarke; G Coates; T Cox; F Cunningham; V Curwen; T Cutts; T Down; R Durbin; X M Fernandez-Suarez; J Gilbert; M Hammond; J Herrero; H Hotz; K Howe; V Iyer; K Jekosch; A Kahari; A Kasprzyk; D Keefe; S Keenan; F Kokocinsci; D London; I Longden; G McVicker; C Melsopp; P Meidl; S Potter; G Proctor; M Rae; D Rios; M Schuster; S Searle; J Severin; G Slater; D Smedley; J Smith; W Spooner; A Stabenau; J Stalker; R Storey; S Trevanion; A Ureta-Vidal; J Vogel; S White; C Woodwark; E Birney
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

6.  The distributed annotation system.

Authors:  R D Dowell; R M Jokerst; A Day; S R Eddy; L Stein
Journal:  BMC Bioinformatics       Date:  2001-10-10       Impact factor: 3.169
  6 in total
  29 in total

Review 1.  Genome and proteome annotation: organization, interpretation and integration.

Authors:  Gabrielle A Reeves; David Talavera; Janet M Thornton
Journal:  J R Soc Interface       Date:  2009-02-06       Impact factor: 4.118

2.  Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.

Authors:  William Speier; Michael F Ochs
Journal:  Bioinformatics       Date:  2012-09-03       Impact factor: 6.937

3.  aGEM: an integrative system for analyzing spatial-temporal gene-expression information.

Authors:  Natalia Jiménez-Lozano; Joan Segura; José Ramón Macías; Juanjo Vega; José María Carazo
Journal:  Bioinformatics       Date:  2009-07-09       Impact factor: 6.937

4.  ProServer: a simple, extensible Perl DAS server.

Authors:  Robert D Finn; James W Stalker; David K Jackson; Eugene Kulesha; Jody Clements; Roger Pettett
Journal:  Bioinformatics       Date:  2007-01-18       Impact factor: 6.937

5.  The Protein Feature Ontology: a tool for the unification of protein feature annotations.

Authors:  Gabrielle A Reeves; Karen Eilbeck; Michele Magrane; Claire O'Donovan; Luisa Montecchi-Palazzi; Midori A Harris; Sandra Orchard; Rafael C Jimenez; Andreas Prlic; Tim J P Hubbard; Henning Hermjakob; Janet M Thornton
Journal:  Bioinformatics       Date:  2008-10-20       Impact factor: 6.937

6.  Protein structure prediction center in CASP8.

Authors:  Andriy Kryshtafovych; Oleh Krysko; Pawel Daniluk; Zinovii Dmytriv; Krzysztof Fidelis
Journal:  Proteins       Date:  2009

7.  Human Proteinpedia: a unified discovery resource for proteomics research.

Authors:  Kumaran Kandasamy; Shivakumar Keerthikumar; Renu Goel; Suresh Mathivanan; Nandini Patankar; Beema Shafreen; Santosh Renuse; Harsh Pawar; Y L Ramachandra; Pradip Kumar Acharya; Prathibha Ranganathan; Raghothama Chaerkady; T S Keshava Prasad; Akhilesh Pandey
Journal:  Nucleic Acids Res       Date:  2008-10-23       Impact factor: 16.971

8.  Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX.

Authors:  Alvaro Martínez Barrio; Erik Lagercrantz; Göran O Sperber; Jonas Blomberg; Erik Bongcam-Rudloff
Journal:  BMC Bioinformatics       Date:  2009-06-16       Impact factor: 3.169

9.  Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

Authors:  Joke Reumers; Joost Schymkowitz; Fréderic Rousseau
Journal:  BMC Bioinformatics       Date:  2009-08-27       Impact factor: 3.169

10.  DASMiner: discovering and integrating data from DAS sources.

Authors:  Diogo F T Veiga; Helena F Deus; Caner Akdemir; Ana Tereza R Vasconcelos; Jonas S Almeida
Journal:  BMC Syst Biol       Date:  2009-11-17
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