Selectome update: quality control and computational improvements to a database of positive selection.
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2014
- doi: 10.1093/nar/gkt1065
- issn: 0305-1048
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S. Moretti et al., « Selectome update: quality control and computational improvements to a database of positive selection. », Serveur académique Lausannois, ID : 10.1093/nar/gkt1065
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Résumé
Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have benchmarked and implemented a thorough quality control procedure on multiple sequence alignments, aiming to provide minimum false-positive results. We have also improved the computational efficiency of the branch-site test implementation, allowing larger data sets and more frequent updates. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees. A total of 6810 gene trees have some evidence of positive selection. Finally, the web interface has been improved to be more responsive and to facilitate searches and browsing.