Selectome


24225318	Selectome update: quality control and computational improvements to a database of positive selection. [PMID: 24225318] Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M. Abstract 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. Nucleic Acids Res. 2014:42(Database issue) \| 44 Citations (from Europe PMC, 2025-03-15)
18957445	Selectome: a database of positive selection. [PMID: 18957445] Proux E, Studer RA, Moretti S, Robinson-Rechavi M. Abstract Genome wide scans have shown that positive selection is relatively frequent at the molecular level. It is of special interest to identify which protein sites and which phylogenetic branches are affected. We present Selectome, a database which provides the results of a rigorous branch-site specific likelihood test for positive selection. The Web interface presents test results mapped both onto phylogenetic trees and onto protein alignments. It allows rapid access to results by keyword, gene name, or taxonomy based queries. Selectome is freely available at http://bioinfo.unil.ch/selectome/. Nucleic Acids Res. 2009:37(Database issue) \| 24 Citations (from Europe PMC, 2025-03-15)

Selectome update: quality control and computational improvements to a database of positive selection. [PMID: 24225318]

Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M.

Abstract

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.

Nucleic Acids Res. 2014:42(Database issue) | 44 Citations (from Europe PMC, 2025-03-15)

Selectome: a database of positive selection. [PMID: 18957445]

Proux E, Studer RA, Moretti S, Robinson-Rechavi M.

Abstract

Genome wide scans have shown that positive selection is relatively frequent at the molecular level. It is of special interest to identify which protein sites and which phylogenetic branches are affected. We present Selectome, a database which provides the results of a rigorous branch-site specific likelihood test for positive selection. The Web interface presents test results mapped both onto phylogenetic trees and onto protein alignments. It allows rapid access to results by keyword, gene name, or taxonomy based queries. Selectome is freely available at http://bioinfo.unil.ch/selectome/.

Nucleic Acids Res. 2009:37(Database issue) | 24 Citations (from Europe PMC, 2025-03-15)

URL:	https://selectome.unil.ch/
Full name:	A Database of Positive Selection
Description:	Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test.
Year founded:	2009
Last update:	2015-5-11
Version:	v6.0
Accessibility:	Accessible
Country/Region:	Switzerland

Data type:	DNA
Data object:	Animal
Database category:	Phylogeny and homology
Major species:	Homo sapiens
Keywords:	branch-site specific likelihood test positive selection

University/Institution:	University of Lausanne
Address:	CH-1015 Lausanne,Switzerland
City:	Lausanne
Province/State:
Country/Region:	Switzerland
Contact name (PI/Team):	Marc Robinson-Rechavi
Contact email (PI/Helpdesk):	selectome@unil.ch

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Database Commons a catalog of worldwide biological databases