Selectome update: quality control and computational improvements to a database of positive selection.
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.
Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland, Evolutionary Bioinformatics group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland, Vital-IT group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland, Computational Phylogenetics group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland, Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK and Swiss National Supercomputing Centre (CSCS), CH-6900, Lugano, Switzerland.
Sébastien
S
Moretti
Balazs
B
Laurenczy
Walid H
WH
Gharib
Briséïs
B
Castella
Arnold
A
Kuzniar
Hannes
H
Schabauer
Romain A
RA
Studer
Mario
M
Valle
Nicolas
N
Salamin
Heinz
H
Stockinger
Marc
M
Robinson-Rechavi
D030561:Databases, Nucleic Acid; D014644:Genetic Variation; D023281:Genomics / Q000592:standards; D006801:Humans; D020407:Internet; D011786:Quality Control; D012641:Selection, Genetic; D016415:Sequence Alignment