Difference between revisions of "ICAR 2011 workshop"
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= Abstract = | = Abstract = | ||
| − | refer to the ABSTRACT #91 on the | + | refer to the ABSTRACT #91 on the [http://www.union.wisc.edu/arabidopsis/materials-2011/Arabidopsis%202011%20Book%20for%20Web%20low-res.pdf abstract book]. |
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Gramene database is a curated resource for comparative functional genomics in crops and model plant | Gramene database is a curated resource for comparative functional genomics in crops and model plant | ||
species. Its strength derives from the integration of genome annotation and functional data with the use of ontologies and by applying a | species. Its strength derives from the integration of genome annotation and functional data with the use of ontologies and by applying a | ||
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association studies (GWAS) currently employ external analysis tools Tassel and Flapjack. Gramene is supported by grants NSF DEB- | association studies (GWAS) currently employ external analysis tools Tassel and Flapjack. Gramene is supported by grants NSF DEB- | ||
0723510, NSF IOS-0703908, and USDA CRIS 1907-21000-030. | 0723510, NSF IOS-0703908, and USDA CRIS 1907-21000-030. | ||
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=Workshop Agenda= | =Workshop Agenda= | ||
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7.30-7.40pm Gramene Database Workshop Introduction (Doreen Ware) | 7.30-7.40pm Gramene Database Workshop Introduction (Doreen Ware) | ||
Revision as of 21:30, 17 June 2011
Contents
Venue
Union Theater
Date and time
June 23, 2011 7:30 pm – 9:00 pm
Abstract
refer to the ABSTRACT #91 on the abstract book.
Gramene database is a curated resource for comparative functional genomics in crops and model plant
species. Its strength derives from the integration of genome annotation and functional data with the use of ontologies and by applying a
phylogenetic framework for genome comparison. In addition to Arabidopsis thaliana and A. lyrata, we host genome browsers for eight
other species spanning a broad taxonomic range. Navigation and visualization tools promote interspecies browsing and the simultaneous
display of multiple species based on whole genome alignments. Gramene additionally provides comparative information in the form of
browsable phylogenetic trees and the assignment of orthology and paralogy relationships. Gramene's genetic diversity database holds
genotype, phenotype, and germplasm data for the major population studies in Arabidopsis. Tools for searching and viewing SNP data
include the display of diversity data in the context of functional impacts on gene structure. Platforms for conducting genome wide
association studies (GWAS) currently employ external analysis tools Tassel and Flapjack. Gramene is supported by grants NSF DEB-
0723510, NSF IOS-0703908, and USDA CRIS 1907-21000-030.
Workshop Agenda
7.30-7.40pm Gramene Database Workshop Introduction (Doreen Ware) 7.40-8.00pm Exploring the Plant Genomes (browse, search, upload personal data, analysis tools) (Josh Stein) 8.00-8.15pm Phylogenetic analysis tools and targeted query tools using Biomart: (Josh Stein and Doreen Ware) 8.15-8.35pm Comparative Pathways Networks and future directions (Pankaj Jaiswal) 8.35-8.50pm Exploring the Plant's Genetic Diversity (Doreen Ware) 8.50-9.00pm Q/A
