ArticleNucleic acids research2017
PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
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- Comparative genomics and genome-wide SNPs of endangered Eld's deer provide breeder selection for inbreeding avoidance.Scientific reports · 2023Article
- The Draft Genome of the "Golden Tide" Seaweed,Genes · 2023Article
- FREEDA: An automated computational pipeline guides experimental testing of protein innovation.The Journal of cell biology · 2023Article
- A high-quality chromosome-level Eutrema salsugineum genome, an extremophile plant model.BMC genomics · 2023Article
- Gene loss during a transition to multicellularity.Scientific reports · 2023Article
- Long-read genome assemblies reveal aZoological research · 2023Article
- Comparative analysis of thyroid hormone systems in rodents with subterranean lifestyle.Scientific reports · 2023Article
- Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution.Botanical studies · 2022Article
- Evidence of episodic positive selection inPeerJ · 2022Article
- Evolutionary genomics and biosynthetic potential of novel environmental Actinobacteria.Applied microbiology and biotechnology · 2021Article
- Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation.Cell reports · 2021Article
- Article
- Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats.Molecular biology and evolution · 2021Article
- Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber.Horticulture research · 2021Article
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4 authors.
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Abstract
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software. We developed the software tool PosiGene that (i) detects positively selected genes (PSGs) on genome-scale, (ii) allows analysis of specific evolutionary branches, (iii) can be used in arbitrary species contexts and (iv) offers visualization of the results for further manual validation and biological interpretation. We exemplify PosiGene's performance using simulated and real data. In the simulated data approach, we determined a false positive rate <1%. With real data, we found that 68.4% of the PSGs detected by PosiGene, were shared by at least one previous study that used the same set of species. PosiGene is a user-friendly, reliable tool for reproducible genome-wide identification of PSGs and freely available at https://github.com/gengit/PosiGene.
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