The Distributed Annotation Service (DAS) at PlantGDB
What is DAS?
DAS (Distributed Annotation System) provides a method for retrieving remotely-served data specific to a genome region, such as "Display all annotations in the range of 10-20kb on Arabidopsis chromosome 1." DAS queries can also limit the types of annotations that are returned, such as "Display only EST_alignments in the range 10-20kb on Arabidopsis chromosome 1."
PlantGDB provides both DAS server (see table below) and DAS client services.
- PlantGDB's DAS server (called "xDAS") delivers genomic alignment data over the internet, so that it to be displayed by genome browser capable of interpreting and displaying DAS data format. All xGDB genome databases at PlantGDB are configured to serve one or more datatypes (see Table I below).
- A DAS client receives, interprets and displays data served by a DAS server. All xGDB genome browsers can display DAS-served data if a source is available (see Table II for available servers).
If you have data tracks you would like to see displayed on a genome browser at PlantGDB, please contact us and we will consider displaying them via our xDAS server.
For detailed instructions on the use of DAS at PlantGDB, visit the PlantGDB Help Pages. For general information on DAS, visit the BioDAS Wiki pages at BioDAS.org.
Table I. PlantGDB DAS servers
| xGDB Database | DAS server URL | DAS Data Sources (DSN) | Available Remote DAS client(s) |
|---|---|---|---|
| AtGDB (Arabidopsis thaliana) |
http://www.plantgdb.org/AtGDB/cgi-bin/das/ | http://www.plantgdb.org/AtGDB/cgi-bin/das/dsn | ATensembl (Ensembl) |
| GmGDB (Glycine max) |
http://www.plantgdb.org/GmGDB/cgi-bin/das/ | http://www.plantgdb.org/GmGDB/cgi-bin/das/dsn | (None at present) |
| PtGDB (Populus trichocarpa) |
http://www.plantgdb.org/PtGDB/cgi-bin/das/ | http://www.plantgdb.org/PtGDB/cgi-bin/das/dsn | PopGenIE (GBrowse) |
| ZmGDB (Chr) (Zea mays) |
http://www.plantgdb.org/ZmGDB/cgi-bin/das/ | http://www.plantgdb.org/ZmGDB/cgi-bin/das/dsn | MaizeGDB.org (Gbrowse) maizesequence.org (Ensembl) |
Table II. Other DAS servers accessible via PlantGDB's DAS client
| Genome Database | DAS server URL | DAS Data Sources (DSN) | Entry Points |
|---|---|---|---|
| Gramene (Ensembl) |
http://www.gramene.org/das/ | http://www.gramene.org/das/dsn | Arabidopsis TAIR8 Populus JGI Sorghum JGI Vitis vinifera 8x Zea mays BAC |
Description of Methods and Subtypes
PlantGDB DAS provides the following types of annotation (also called annotation features) : EST, cDNA, and yrGATE (see table I above).
Annotations can also be queried by their subtype or method of creation. Annotations of type EST derived from GeneSeqer_cognate and GeneSeqer_noncognate methods. Annotations of type cDNA are derived from GeneSeqer_cognate and GeneSeqer_noncognate methods. Annotations of type yrGATE are derived from yrGATE Community Annotations.
GeneSeqer is a program that creates spliced alignments of expressed sequences to a genome sequence (for more information, refer to: Brendel, V., Xing, L. & Zhu, W. (2004). Gene structure prediction from consensus spliced aligment of multiple ESTs matching the same genomic locus. Bioinformatics 20, 1157-1169.)
PlantGDB DAS Service provides high quality spliced alignments, those with similarity and coverage scores greater or equal to 0.8.
In cases where a single EST can have multiple high scoring spliced alignments, the cognate/noncognate distinction serves as a point of further classification.
Cognate refers to the most probable genome location for an EST's origin, which is defined as the spliced alignment(s) with the maximum product of similarity and coverage scores among all such products of spliced alignments of a given EST.
Other spliced alignments, that are not maximally scoring, are designated noncognate. For further information about cognate and noncognate types of spliced alignment, please consult Zhu,W., Schlueter,S.D. and Brendel,V. (2003). Refined annotation of the Arabidopsis thaliana genome by complete EST mapping. Plant Physiol., 132, 469-484.