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Protocols

Selectome specifications

Information


Unique identifier OMICS_21204
Name Selectome
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Sebastien Moretti

Publications for Selectome

Selectome citations

 (9)
library_books

Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans

2017
Mol Biol Evol
PMCID: 5435107
PMID: 28333345
DOI: 10.1093/molbev/msx083

[…] We use gene sets from NCBI Biosystems () (see next section). Since these sets are annotated with Entrez gene IDs, whereas Selectome uses Ensembl gene IDs, we created a one-to-one Ensembl–Entrez conversion table, to map the Ensembl gene IDs in the branch specific gene tables (Gi) to Entrez gene IDs. First, we started with […]

library_books

Comprehensive transcriptional map of primate brain development

2016
Nature
PMCID: 5325728
PMID: 27409810
DOI: 10.1038/nature18637

[…] to a background set of all 1,848 variable genes. Gene paralogs were downloaded from Ensembl with BioMart. We checked genes for evidence of positive selection on different evolutionary branches using Selectome, (http://selectome.unil.ch/). […]

library_books

Extracting functional trends from whole genome duplication events using comparative genomics

2016
PMCID: 4862183
PMID: 27168732
DOI: 10.1186/s12575-016-0041-2

[…] ces are then placed within gene families based on a clustering algorithm such as single-linkage clustering. Pre-established gene families from gene family databases such as Ensembl [], TAED [, ], and Selectome [] may also be used, to which new sequences can be added using software like pplacer []. Multiple sequence alignments are generated using standard alignment algorithms which incorporate prog […]

call_split

Tissue Specific Evolution of Protein Coding Genes in Human and Mouse

2015
PLoS One
PMCID: 4488272
PMID: 26121354
DOI: 10.1371/journal.pone.0131673
call_split See protocol

[…] Brawand et al. RNA-seq []. The corresponding results are presented in .As measures of evolutionary rate of protein-coding genes, we used the estimates from the branch-site model [] as precomputed in Selectome []: purifying selection estimated by the dN/dS ratio ω0 on the proportion of codons under purifying selection (noted "Omega" in the figures), evidence for positive selection estimated by the […]

library_books

Human Chromosome Y and Haplogroups; introducing YDHS Database

2015
PMCID: 4477006
PMID: 26061870
DOI: 10.1186/s40169-015-0060-7

[…] ovide valuable information when the deleterious potential of a mutation is otherwise difficult to assess.We also provide information whether the gene of interest is under positive selection using the Selectome database (http://selectome.unil.ch/). In addition, we provide information regarding repeats for the gene of interest via UCSC genome tracks. The location and population of the highest freque […]

library_books

Understanding the functional difference between growth arrest specific protein 6 and protein S: an evolutionary approach

2014
Open Biol
PMCID: 4221892
PMID: 25339693
DOI: 10.1098/rsob.140121

[…] st. Sites can be classified under relax and strict thresholds of BEB score > 0.95 and BEB score > 0.99, respectively.The codons under positive selection between GAS6 and PROS1 were retrieved from the Selectome database of precomputed tests of positive selection [,], which uses the branch-site model from CodeML/PAML. In Selectome, we focused solely on the branch named ‘Euteleostomi’ (which correspo […]

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Selectome institution(s)
Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland; Evolutionary Bioinformatics group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Computational Phylogenetics group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK; Swiss National Supercomputing Centre (CSCS), Lugano, Switzerland
Selectome funding source(s)
Supported by Project UNIL.5 (Grid/Selectome) of the ‘AAA/SWITCH– e-infrastructure for e-science’ program; the Swiss Platform for High-Performance and High-Productivity Computing (HP2C); the Swiss National Science Foundation [31003A 133011/1 and CR32I3_143768]; Etat de Vaud; Fondation du 450eme anniversaire de l’Universite de Lausanne and Swiss National Science Foundation [132476 and 136477].

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