Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

A CONCEPTUAL FRAMEWORK FOR COMPARISON OF EST SETS AND ITS APPLICATION IN THE FLORAL GENOME PROJECT

¹ Department of Biology, Pennsylvania State University, University Park, PA 16801, USA

² Department of Statistics, Pennsylvania State University, University Park, PA 16801, USA

³ Molecular Evolution and Bioinformatics CEH Oxford, Mansfield Road Oxford OX1 3SR, UK

EST sets are now available for a wide range of plant species. Moreover, for many species, EST sets are the only available genomic resource. We provide a framework for describing and comparing EST sets across organs or developmental stages for a single species and for comparing EST sets across species. By estimating parameters that describe the sampling properties for the EST sets being compared, we can make accurate estimates of the frequency of overlap in expressed gene families. At the same time, the evolutionary relationships among observed ESTs representing a particular gene family are inferred through phylogenetic analyses on alignments of ESTs and publicly available full-length sequences. Due to the incomplete nature of EST sequences, the inferred evolutionary relationships should be interpreted with caution. With this caveat in mind, clones may be identified for further investigation based the results of phylogenetic analyses. We demonstrate the utility of our conceptual framework in a comparative analysis of floral EST sets. This research is supported by an NSF Plant Genome Research grant.