Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

The Comparative Map And Trait Viewer (CMTV): Visual Integration Of Disparate And Dispersed Genomic Data

Andrew Farmer¹ , Mark Sawkins² , Guy Davenport² , Christelle Bencivenni ² , Jean-Marcel Ribaut³

¹  National Center for Genome Resources 2935 Rodeo Park Dr E Santa Fe, NM 87508 USA

²  CIMMYT Apartado Postal 6-641 06600 Mexico D.F. Mexico

³  Generation Challenge Program c/o CIMMYT Apartado Postal 6-641 06600 Mexico D.F. Mexico

Plant Biologists have access to a wealth of data for which the genomic context provides a natural framework for comparing results from different experiments and across different genetic backgrounds and species. Although many different web-sites exist for different types of data from different species, there is a clear need for software that provides the researcher with the ability to collect and integrate disparate genomic, genetic and phenotypic data.
The Comparative Map and Trait Viewer (CMTV) is an open source Java interface for:

• Collecting genomic map and disparate map-related data (e.g. QTLs, gene expression values, sequence data) from dispersed sources including local flatfiles, remote public databases, and analysis tools;
  
• Utilizing corresponding mapped loci between different maps in order to:
  
  
  
  • construct consensus maps combining results over multiple experiments;
    
  • leverage comparative genomic data in syntenic areas from multiple species, or duplicated regions within the same genome;
    
  • combine project data with previously published experiments into a common reference map.
    
  
  
• Creating highly interactive visualizations of the collected data that help enable biological discovery through a variety of functions such as grouping, sorting, and filtering that operate on the biological attributes of the underlying data