|
|
| Home |
| EST Assembly |
| GSS Assembly |
|
|
| Publications |
| Mailing List |
| Acknowledgements |
| Site Map |
| F.A.Q. |
| Links |
PlantGDB DAS ServiceNOTE (May 16): We are working to upgrade our DAS service over the next several weeks; thanks for your patience!A subset of PlantGDB annotation data is accessible through the Distributed Annotation System (DAS). DAS provides a method for retrieving data specific to a genome region, such as annotations in the range 10-20kb on Arabidopsis chromosome 1. DAS queries can also limit the types of annotations that are returned, such as only EST_alignments in the range 10-20kb on Arabidopsis chromosome 1. Usage of DAS is appropriate for downloading annotation information for specific regions, for importing PlantGDB data into genome browsers for viewing, and for other external DAS clients. One example is NASC's Arabidopsis Ensembl browser, which can import PlantGDB Arabidopsis annotation data through 'manage DAS sources'. PlantGDB DAS provides the following types of annotation (also called annotation features) : EST_alignment, cDNA_alignment, and Gene. Annotations can also be queried by their subtype or method of creation. Annotations of type EST_alignment derived from GeneSeqer_cognate and GeneSeqer_noncognate methods. Annotations of type cDNA_alignment are derived from GeneSeqer_cognate and GeneSeqer_noncognate methods. Annotations of type Gene are derived from UCA_manual_curation. This allows more specific queries of PlantGDB data, such as only the noncognate EST alignments in the range 10-20 kb on Arabidopsis chromosome 1. Description of Methods and Subtypes 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. UCA_manual_creation denotes that the gene was created with the User Contributed Annotation Tool, which is a web based manual gene annotation tool for use in community databases. To learn more about the manually curated UCA (User Contributed Annotation) data please consult: Schlueter, S.D., Wilkerson, M.D., Huala, E., Rhee, S.Y. & Brendel, V. (2005) Community-based gene structure annotation for the Arabidopsis thaliana genome. Trends Plant Sci. 10, 9-14. Information for accessing DAS To view databases available through DAS, also called data sources: http://www.plantgdb.org/cgi-bin/das/dsn Example queries: Query for a list of the genome segments that have annotation data: http://www.plantgdb.org/cgi-bin/das/atgdb5/entry_points
http://www.plantgdb.org/cgi-bin/das/atgdb5/features?segment=1:500,6000
http://www.plantgdb.org/cgi-bin/das/atgdb5/features?segment=1:500,6000&type=EST_alignment
http://www.plantgdb.org/cgi-bin/das/atgdb5/features?segment=1:500,6000&type=EST_alignment:GeneSeqer_cognate
Comments and questions should be directed to PlantGDB. |
