MERCATOR is an orthology mapping program suitable for multiple genomes.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.
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Colin N. Dewey, Peter M. Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
Parametric Alignment of Drosophila Genomes
PLoS Comput Biol 2(6): e73. doi:10.1371/journal.pcbi.0020073