• Intro

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  • Credits

    UC Davis

    Project overview. Library construction and sequencing.
    Data processing, storage and analysis.

    The Compositae Genome Project http://compgenomics.ucdavis.edu/ aims to:

  • Generate an extensive expressed sequence tag (EST) database from two different genotypes each of lettuce and sunflower.

  • Determine the extent of synteny among sunflower, lettuce and Arabidopsis.

  • Develop PCR-based markers for high-throughput genetic analyses.

  • The initial phase of this project is complete. Over 60,000 lettuce and 40,000 sunflower ESTs have been sequenced from multiple cDNA libraries.

    ESTs have been assembled using the CAP3 program and organized into the Compositae Genome Project database (CGPDB) http://cgpdb.ucdavis.edu/. This assembly represents about 19,000 lettuce and 12,000 sunflower unigenes.

    mySQL http://www.mysql.com/ was chosen as an efficient tool to manage the data. Custom PHP http://www.php.net/ and Python http://www.python.org/ programs were developed with publicly available phpMyAdmin software http://www.phpmyadmin.net/ to manipulate the data and visualize the assemblies.