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Abstract Detail

Modeling and Computational Biology

Mueller, Lukas [1], Menda, Naama [2], Buels, Robert [2], Kreuter, Marty [2], Mills, Adri [2], Skwarecki, Beth [2], Carpita, Chris [2], Tanksley, Steve [2].

The SOL Genomics Network - a clade oriented database for the Solanaceae and related Asterids.

The Solanaceae Genomics Network (SGN, http://sgn.cornell.edu/) is clade-oriented database (COD) focusing on the plants of the nightshade family, including tomato, potato, pepper and eggplant, and is one of the bioinformatics nodes of the international tomato genome sequencing project. The COD paradigm attempts to integrate several related species into one resource, providing a better framework for comparative queries and a better phylogenetic context. In addition to the emerging tomato genome sequence and its annotation, SGN contains a large number of EST sequences which have been clustered into unigenes and extensively annotated. As part of the COD framework, the sequences have been clustered into gene families, for which alignments and trees have been pre-calculated and can be browsed on-line using the SGN alignment viewer and tree browser. The extensive mapping data is presented in a clade-oriented format using the interactive SGN comparative mapviewer. SGN houses the master database of the Conserved Ortholog Set (COS) markers, which form the basis for many comparative studies and have been used extensively to construct some of the maps available on SGN. Extensive biochemical pathway information is available for selected Solanaceae species in the solcyc databases, a collection of pathway genome databases that are similar to AraCyc. Recently, SGN introduced a locus database, creating a central reference database for Solanaceae locus names and descriptions, and a phenotype database, presenting the uniquely rich and extensive phenotypic data available for the Solanaceae, and allowing to relate the phenotypes to genotype data. Both databases can be updated by the SGN user community, who can supply descriptions, images and other data through easy to use interfaces on the web, and thus create a truly community driven database.

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Related Links:

1 - Cornell University, Department of Plant Breeding and Genetics, Emerson Hall, Ithaca, NY, 14853, USA
2 - Cornell University, Department of Plant Breeding and Genetics

tomato genome.

Presentation Type: Plant Biology Abstract
Session: P
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM
Number: P41006
Abstract ID:576

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