Algorithms for Constructing Comparative Maps

Abstract

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. In this paper we present efficient algorithms that help in automating this effort and offer an explicit set of principles on which to base the construction of such maps. We compare the results of three approaches: manual expert analysis, a simple linear algorithm, and a more comples stack-based algorithm. All three methods produce remarkably similar results, with the stack algorithm more closely approximating the manual expert analysis.