1 / 37

Map Curation on GrainGenes

Explore curated maps and raw data on GrainGenes database, including genetic and physical loci mapping in wheat and barley, with access to articles and interactive tools.

beatricem
Download Presentation

Map Curation on GrainGenes

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003

  2. The Maps and Map Data page has links to articles, raw data and line maps

  3. ‘Map’ of CS x Cheyenne Disomic Substitution

  4. Raw Mapping data of CS x Cheyenne Disomic Substitution

  5. The Maps and Map Data page has links to articles, raw data and line maps

  6. Web Summary of Interactive Maps links to the GrainGenes database

  7. Flavors of GrainGenes Maps Genetic: Loci mapped by recombination frequency in Synthetic x Opata

  8. Flavors of GrainGenes Maps Consensus: combined maps of hexaploid wheat by Sorrells et al. Highlighted loci have best BLAST hits.

  9. Wheat and Barley Public EST Resources 600,000 500,000 400,000 Wheat Number of ESTs 300,000 Barley 200,000 100,000 0 Jan-01 Jan-02 Jan-03 Sep-00 Sep-01 Sep-02 Sep-03 May-00 May-01 May-02 May-03 Date

  10. Flavors of GrainGenes Maps Physical: loci mapped by physical placement on a chromosome. This is a deletion map from the U.S. wheat genome project.

  11. Sequence Records from the NSF ESTs contain the supporting data and links to maps supported by other projects:

  12. QTL map from a barley malting quality study

  13. Interactive Map Construction • Identify relevant maps from the literature, • usually from Theoretical and Applied Genetics • find Reference Keyword=map* & Year=2002 • results in 186 objects • Contact authors to acquire raw data and • a spreadsheet with loci and chromosome • positions

  14. Convert locus names to • GrainGenes standardized • nomenclature

  15. Check all loci to be sure a probe record exists • Create probe records for new loci • involves going to references within the paper • contact with authors • can be very time consuming!!! • Create other object records • genes, germplasm, colleague, reference etc. A map set takes ~ a week if all goes smoothly and authors cooperate.

  16. The Genome Browser (GBrowse) is a new map viewing tool.

  17. Click on a Bin bar to see all loci mapped to that region

  18. Click on a Probe ESTs link to access query features on wEST

  19. The CMAP viewer will allow users to compare maps.

  20. NCBI is importing GrainGenes records for the Entrez Map View Tool.

  21. Maps for Education

  22. In-Depth pages will provide links to PubMed literature searches, NCBI, GrainGenes, etc.

More Related