Distributed Annotation System
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 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
- The DAS registration server
- Ensembl The Ensembl Genome Browser
- UCSC Genome Browser
- WormBase
- FlyBase
- TIGR
- ProServer
- SUPERFAMILY
- InterPro
- SIMAP
DAS clients
| Name | Description | Links |
|---|---|---|
| BioJava DAS Client | ||
| Dasty | A web client for visualizing protein sequence feature information using DAS | |
| 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 | |
| Geodesic | An stand-alone Java application | |
| 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 | |
| Jalview | A multiple sequence alignment editor & viewer | |
| OmniGene | The user interface is based on the EnsEMBL interface | |
| SIMAP | Similarity Matrix of Proteins | |
| SPICE | A browser for the annotations for protein sequences and structures | |
| STRAP | Underlining sequence features in multiple alignments. Example output: | |
| TIGR DAS Viewer | ||
| WormBase | The WormBase genome Browser. Includes a DAS viewer named DASView |
References
- 1 2 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. - ↑ 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.
- ↑ 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.
- ↑ The DAS/2 Protocol. BioDAS.
External links
This article is issued from Wikipedia - version of the 6/29/2016. The text is available under the Creative Commons Attribution/Share Alike but additional terms may apply for the media files.