ICAR 2011 workshop

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Union Theater, Madison, Wisconsin

Date and time

June 23, 2011 7:30 pm – 9:00 pm


Refer to the ABSTRACT #91 on the abstract book.

Gramene database (www.gramene.org) 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.

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

Workshop material

Gramene website/database

Visit the project database website at http://www.gramene.org


View/download the Gramene Brochure File:ICAR 2011 Gramene.pdf

Presentation files

Gramene Tutorials

  ^These may be human genome Ensembl centric, however the tools and options work similarly on Plant Ensembl genomes hosted by Gramene.


We thank the ICAR 2011 organizers for providing us an opportunity to organize the Gramene workshop. The project is supported by grants NSF DEB-0723510, NSF IOS-0703908, and USDA CRIS 1907-21000-030.