Recommended
Recommended
More Related Content
What's hot
What's hot (20)
Similar to Chestnut Resources via Hardwood Genomics Web
Similar to Chestnut Resources via Hardwood Genomics Web (20)
Recently uploaded
Recently uploaded (20)
Chestnut Resources via Hardwood Genomics Web
- 1. ChestnutResourcesviathe HardwoodGenomicsWeb Meg Staton University of Tennessee Department of Entomology and Plant Pathology
- 2. Overview Databases and Websites – the infrastructure to deal with the data deluge and make the resources useful Hardwood Genomics Content Hardwood Genomics Tools Tripal – the database software
- 3. Hardwood Genomics Web www.hardwoodgenomics.org • Website for hardwood tree data • Transcriptomes • Whole Genomes • Genetic and Physical Maps • Populations • Phenotypes • Genotypes
- 4. Software tools to find and explore information Organism Page mRNA Page Genome Page BLAST Search Keyword Search Symap Search Pages with information to explore and download
- 8. Genes -> mRNAs transcripts • Genes – the functional units of the genome • Can produce more than one type of transcript • (Isn’t biology cool!?!) • Chinese Chestnut genome has about • 36,478 genes • 38,146 transcripts
- 9. mRNA Page
- 10. mRNA Page
- 11. mRNA Page
- 12. Chestnut Genome • Chestnut has an estimated 800,000,000 bases of DNA • We have sequenced the chestnut genome and placed it into 41,260 pieces covering 724Mb • Equivalent to a 500,000 page book • Not recommended for light reading! • Nathaniel Cannon’s work is putting these pieces in order 41,260
- 13. Ways to access the Chestnut genome - Download • Download the raw sequence files: 41,260 of these
- 14. Genome Page
- 15. Genome Page
- 16. Genome Page
- 17. TOOLS
- 18. Ways to access the Chestnut genome • This 500,000 page file isn’t too useful… • What does it do? Where are the genes??? I could really use a map!!!
- 19. Ways to access the Chestnut genome
- 20. Examine a portion of the total genome
- 22. Visualizes the location of genes in “tracks”
- 23. Visualizes the alignment of genes that originate from other plants such as peach and Arabidopsis
- 24. Can select an mRNA to get more information
- 25. BLAST • Bring your own sequence of interest • Run BLAST • Compare to •Chestnut mRNAs •Chestnut proteins
- 26. BLAST
- 29. Other ways to find what you need and cool stuff to do • Searching • Search by gene name • Search by function • “Cytochrome P450” • “Mitogen-activated protein kinase” • Gene annotation • Think we did a bad job for the “map” of this gene? You can go fix it!
- 30. Other ways to find what you need and cool stuff to do Symap • Compare the structure of the chestnut genome to other trees
- 31. TRIPAL SOFTWARE
- 32. A web framework for genetic and genomic data Goals: Simplify construction of a community genomics websites Enable individual labs or research communities Encourage high-quality, standards-based websites for data sharing and collaboration Expand and reuse code
- 35. Why use Tripal? • Open source • Friendly developers • Responsive mailing list • Much of the stuff you need for a website is already there Modules: • Organisms • Genomes • Transcriptomes • Stocks/Germplasm • Phenotypes • Genotypes
- 36. NSF DIBBS Grant • By leveraging the needs across many plant genomic communities, we can make a strong case for federal support • Funded development helps everyone! • DIBBS: Integrate Tripal with Galaxy, an open source, web-based platform for data intensive biomedical research. Stephen Ficklin
- 37. Jack Davitt Nathan Henry Ming Chen Former Research Associate Research Associate Graduate Student
Editor's Notes
- Developing High-Throughput Bioinformatic Pipelines for Cross-Disciplinary Research at an Ag University: Case Studies in Dog, Chicken, and Hardwood Trees
- Overview Perspectives from a core facility Examples GWAS Whole genome resequencing RNA sequencing Training Research Chestnut blight resistance Comparative genomics of hardwood trees