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PMID: 17850653 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Integrating sequence and structural biology with DAS.

BMC bioinformatics ·Vol. 8 ·2007-09-12 ·Pages 333

Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A, Hubbard TJ

Abstract

The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.

MeSH Terms
Algorithms Chromosome Mapping/methods Computational Biology/methods Database Management Systems Databases, Genetic Information Storage and Retrieval/methods Internet Sequence Analysis/methods Systems Integration User-Computer Interface
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Prlić Andreas
The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK. [email protected]
Down Thomas A
Kulesha Eugene
Finn Robert D
Kähäri Andreas
Hubbard Tim J P
References (30)
30 references, click to expand
  1. Integrating electron microscopy information into existing Distributed Annotation Systems.
    J Struct Biol. 2007 May;158(2):205-13 PMID: 17400476
  2. The Jalview Java alignment editor.
    Bioinformatics. 2004 Feb 12;20(3):426-7 PMID: 14960472
  3. CARGO: a web portal to integrate customized biological information.
    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W16-20 PMID: 17483515
  4. iHOP web services.
    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W21-6 PMID: 17485473
  5. New tools and expanded data analysis capabilities at the Protein Structure Prediction Center.
    Proteins. 2007;69 Suppl 8:19-26 PMID: 17705273
  6. WormBase: network access to the genome and biology of Caenorhabditis elegans.
    Nucleic Acids Res. 2001 Jan 1;29(1):82-6 PMID: 11125056
  7. ProSup: a refined tool for protein structure alignment.
    Protein Eng. 2000 Nov;13(11):745-52 PMID: 11161105
  8. The generic genome browser: a building block for a model organism system database.
    Genome Res. 2002 Oct;12(10):1599-610 PMID: 12368253
  9. BioMOBY: an open source biological web services proposal.
    Brief Bioinform. 2002 Dec;3(4):331-41 PMID: 12511062
  10. LGA: A method for finding 3D similarities in protein structures.
    Nucleic Acids Res. 2003 Jul 1;31(13):3370-4 PMID: 12824330
  11. INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis.
    Nucleic Acids Res. 2003 Jul 1;31(13):3468-70 PMID: 12824346
  12. Biological SOAP servers and web services provided by the public sequence data bank.
    Nucleic Acids Res. 2003 Jul 1;31(13):3836-9 PMID: 12824432
  13. The distributed annotation system.
    BMC Bioinformatics. 2001;2:7 PMID: 11667947
  14. Protein structure comparison by alignment of distance matrices.
    J Mol Biol. 1993 Sep 5;233(1):123-38 PMID: 8377180
  15. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
    Protein Eng. 1998 Sep;11(9):739-47 PMID: 9796821
  16. An HMM posterior decoder for sequence feature prediction that includes homology information.
    Bioinformatics. 2005 Jun;21 Suppl 1:i251-7 PMID: 15961464
  17. SOAP-based services provided by the European Bioinformatics Institute.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W25-8 PMID: 15980463
  18. Integrating protein annotation resources through the Distributed Annotation System.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W468-70 PMID: 15980514
  19. Dasty and UniProt DAS: a perfect pair for protein feature visualization.
    Bioinformatics. 2005 Jul 15;21(14):3198-9 PMID: 15905273
  20. Adding some SPICE to DAS.
    Bioinformatics. 2005 Sep 1;21 Suppl 2:ii40-1 PMID: 16204122
  21. Pfam: clans, web tools and services.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51 PMID: 16381856
  22. E-MSD: improving data deposition and structure quality.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D287-90 PMID: 16381867
  23. Critical assessment of methods of protein structure prediction (CASP)--round 6.
    Proteins. 2005;61 Suppl 7:3-7 PMID: 16187341
  24. Taverna: a tool for building and running workflows of services.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W729-32 PMID: 16845108
  25. XML schemas for common bioinformatic data types and their application in workflow systems.
    BMC Bioinformatics. 2006;7:490 PMID: 17087823
  26. SISYPHUS--structural alignments for proteins with non-trivial relationships.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D253-9 PMID: 17068077
  27. Ensembl 2007.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7 PMID: 17148474
  28. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12 PMID: 17170002
  29. New developments in the InterPro database.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8 PMID: 17202162
  30. ProServer: a simple, extensible Perl DAS server.
    Bioinformatics. 2007 Jun 15;23(12):1568-70 PMID: 17237073
Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-8-333
Email
[email protected]
Published
2007-09-12
Epub
2007-00-12
Pages
333
Language
English
Region
England
NLM ID
100965194
PMCID
PMC2031907
Subset
IM
Grants
Wellcome Trust · 062023 · United Kingdom
Wellcome Trust · 077198 · United Kingdom
External Links
PubMed source DOI: 10.1186/1471-2105-8-333 PMC Full Text View journal details
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