Mercator cliques


Multiple Whole-Genome Orthology Map Construction

Colin Dewey, Lior Pachter

[Introduction] [Methods] [Maps/Alignments] [Source Code] [References]


Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous", "orthologous", and "paralogous" instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence. Here we present our initial work in the form a program called Mercator that constructs orthology maps between multiple whole genomes.


Our basic strategy in building homology maps is to use exons that are orthologous in multiple genomes as map "anchors." Given K genomes, the steps in the map construction are as follows:


Source Code

Mercator is free software under the GNU General Public License and is available as part of Colin Dewey's source code distribution.

Binaries may be made available upon request.