UVPAR: fast detection of functional shifts in duplicate genes

Background: The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. Results: We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of the proteins encoded by couples of duplicate genes in two different species, UVPAR detects the regions in which modifications of the functional constraints in the paralogs occurred since both species diverged. Sequences can be analyzed with UVPAR in just a few minutes on a standard PC computer. To demonstra...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Vicente Arnau, Miguel Gallach, J. Ignasi Lucas, Ignacio Marín
• Keywords: BMCBI 2006, Duplicate Genes, Functional Constraints, Sequences