Plant & Animal Genome IX Conference

Workshop: Bioinformatics/Computers
W15_04.html

AN AUTOMATED METHOD FOR CONSTRUCTING COMPARATIVE MAPS

¹ Center for Applied Mathematics, Cornell University, Ithaca, NY 14853, USA.

² Department of Computer Science, Cornell University, Ithaca, NY 14853, USA.

³ Department of Plant Breeding, Cornell University, Ithaca, NY 14853, USA.

Comparative maps are a powerful tool for aggregating genetic information about related organisms, for inferring phylogenetic relationships, and for examining hypotheses about the evolution of gene families and the functional significance of orthologous genes. Construction of any genetic map is laborious, but compiling comparative maps across multiple species requires a large investment of manual effort on the part of biologists. Additionally, biologists from different labs often use differing rules which are often not quantified or made precise in the literature, making it difficult to understand how the various comparative maps relate to one another. We offer a rigorous definition for the process of constructing comparative maps that is based on fundamental principles. From this we have developed a robust, efficient algorithm which automates the identification of homeologous (syntenic) segments and construction of comparative maps. Results have been evaluated for diverse pairs of species, and closely approximate the manual expert analysis. We have incorporated this algorithm into a tool which is now available in a preliminary version. For input, it requires the positions of the markers of one species, as well as the location of homologs to each marker in the second species. Output is given both graphically and in text form. Only a single parameter is required, which carries a simple biological explanation. Our program allows comparative maps to be constructed in a few minutes.