UVPAR: fast detection of functional shifts in duplicate genes
<p>Abstract</p> <p>Background</p> <p>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 underlyin...
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| Format: | Article |
| Language: | English |
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BMC
2006-03-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/7/174 |
| _version_ | 1819088457136340992 |
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| author | Lucas J Ignasi Gallach Miguel Arnau Vicente Marín Ignacio |
| author_facet | Lucas J Ignasi Gallach Miguel Arnau Vicente Marín Ignacio |
| author_sort | Lucas J Ignasi |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Hox </it>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 <it>Danio rerio </it>and for the gene <it>Ariadne-2</it>.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-21T21:52:20Z |
| format | Article |
| id | doaj.art-80706949c36e42f48bdf8b2cb10c49c1 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T21:52:20Z |
| publishDate | 2006-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-80706949c36e42f48bdf8b2cb10c49c12022-12-21T18:49:03ZengBMCBMC Bioinformatics1471-21052006-03-017117410.1186/1471-2105-7-174UVPAR: fast detection of functional shifts in duplicate genesLucas J IgnasiGallach MiguelArnau VicenteMarín Ignacio<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Hox </it>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 <it>Danio rerio </it>and for the gene <it>Ariadne-2</it>.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/7/174 |
| spellingShingle | Lucas J Ignasi Gallach Miguel Arnau Vicente Marín Ignacio UVPAR: fast detection of functional shifts in duplicate genes BMC Bioinformatics |
| title | UVPAR: fast detection of functional shifts in duplicate genes |
| title_full | UVPAR: fast detection of functional shifts in duplicate genes |
| title_fullStr | UVPAR: fast detection of functional shifts in duplicate genes |
| title_full_unstemmed | UVPAR: fast detection of functional shifts in duplicate genes |
| title_short | UVPAR: fast detection of functional shifts in duplicate genes |
| title_sort | uvpar fast detection of functional shifts in duplicate genes |
| url | http://www.biomedcentral.com/1471-2105/7/174 |
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