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UVPAR: fast detection of functional shifts in duplicate genes

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UVPAR: fast detection of functional shifts in duplicate genes

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dc.contributor.author Arnau Llombart, Vicente
dc.contributor.author Gallach Caballero, Miguel
dc.contributor.author Lucas Lledó, José Ignacio
dc.contributor.author Marín Lozano, Ignacio
dc.date.accessioned 2015-06-26T08:37:07Z
dc.date.available 2015-06-26T08:37:07Z
dc.date.issued 2006
dc.identifier.citation Arnau Llombart, Vicente ; Gallach Caballero, Miguel ; Lucas Lledó, José Ignacio ; Marín Lozano, Ignacio (2006) UVPAR: fast detection of functional shifts in duplicate genes. Bmc Bioinformatics 7 174(1) 174(12)
dc.identifier.uri http://hdl.handle.net/10550/44756
dc.description.abstract 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 demonstrate the power of the program, we first show how the results obtained with UVPAR compare to those based on other approaches, using data for vertebrate Hox genes. We then describe a comprehensive study of the RBR family of ubiquitin ligases in which we have performed 529 analyses involving 14 duplicate genes in seven model species. A significant increase in the number of functional shifts was observed for the species Danio rerio and for the gene Ariadne-2. Conclusion These results show that UVPAR can be used to generate sensitive analyses to detect changes in the selection constraints acting on paralogs. The high speed of the program allows its application to genome-scale analyses.
dc.language.iso eng
dc.relation.ispartof Bmc Bioinformatics, 2006, vol. 7, p. 174(1)-174(12)
dc.subject genètica
dc.title UVPAR: fast detection of functional shifts in duplicate genes
dc.type journal article es_ES
dc.date.updated 2015-06-26T08:37:08Z
dc.identifier.doi 10.1186/1471-2105-7-174
dc.identifier.idgrec 035517
dc.rights.accessRights open access es_ES

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