Distributed Annotation System

From Wikipedia, the free encyclopedia
Jump to: navigation, search

The Distributed Annotation System (DAS) is an open source project that is used in bioinformatics to share and collate genomic annotation information.[1][2][3] It first originated as the work of Robin Dowell, Rodney Jokerst, Allen Day, Sean Eddy and Lincoln Stein,[1] but it has since evolved into a community driven project with its main hub BioDAS. The current stable version of DAS is 2.0, which is also written as "DAS/2", whereas the older but still commonly used version 1.6 is abbreviated as "DAS/1". The latter DAS/2 specification is not compatible with DAS/1.[4]

Sites and tools currently using DAS[edit]

DAS clients[edit]

Name Description Links
BioJava DAS Client
Dasty A web client for visualizing protein sequence feature information using DAS [1] [2]
DasView A server-side Perl application. This tool is mentioned in the original DAS publication, but has subsequently disappeared.
EnsEMBL The EnsEMBL Genome Browser. Provides built-in support for DAS [3]
Geodesic An stand-alone Java application [4]
IGB The Integrated Genome Browser (IGB, pronounced "ig-bee") is an application built upon the GenoViz SDK and Genometry for visualization and exploration of genomes and corresponding annotations from multiple data sources [5]
Jalview A multiple sequence alignment editor & viewer [6]
OmniGene The user interface is based on the EnsEMBL interface [7] [8]
SIMAP Similarity Matrix of Proteins [9] [10]
SPICE A browser for the annotations for protein sequences and structures [11] [12] [13]
STRAP Underlining sequence features in multiple alignments. Example output: [14] [15]
TIGR DAS Viewer [16]
WormBase The WormBase genome Browser. Includes a DAS viewer named DASView
Edit this table

References[edit]

  1. ^ a b Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L (2001). "The distributed annotation system.". BMC Bioinformatics 2: 7. doi:10.1186/1471-2105-2-7. PMC 58584. PMID 11667947. 
  2. ^ Finn RD, Stalker JW, Jackson DK, Kulesha E, Clements J, Pettett R (2007). "ProServer: a simple, extensible Perl DAS server.". Bioinformatics 23 (12): 1568–70. doi:10.1093/bioinformatics/btl650. PMC 2989875. PMID 17237073. 
  3. ^ Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlic A (2008). "Integrating biological data - the Distributed Annotation System.". BMC Bioinformatics. 9. Suppl 8: S3. doi:10.1186/1471-2105-9-S8-S3. PMC 2500094. PMID 18673527. 
  4. ^ The DAS/2 Protocol. BioDAS.

External links[edit]