ArticlePloS one2013
The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 43 citations in OpenAlex.
- OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches.Bioinformatics (Oxford, England) · 2021Article
- Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes.Briefings in bioinformatics · 2021Article
- 'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.NAR genomics and bioinformatics · 2020Article
- Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.Bioinformatics (Oxford, England) · 2019Article
- OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.Genomics, proteomics & bioinformatics · 2017Article
- SMORE: Synteny Modulator of Repetitive Elements.Life (Basel, Switzerland) · 2017Article
- Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes.BMC genomics · 2017Article
- Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny.Briefings in bioinformatics · 2017Article
- Article
- Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.BMC genomics · 2016Article
- Homoeologs: What Are They and How Do We Infer Them?Trends in plant science · 2016Review
- Standardized benchmarking in the quest for orthologs.Nature methods · 2016Article
- Inferring Orthologs: Open Questions and Perspectives.Genomics insights · 2016Review
- Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma.PloS one · 2016Article
- Improved orthologous databases to ease protozoan targets inference.Parasites & vectors · 2015Article
- Insect phylogenomics.Insect molecular biology · 2015Review
- Comparative Genomics of Listeria Sensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer.Genome biology and evolution · 2015Article
- Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.Journal of molecular evolution · 2015Article
- Phylogenomics with paralogs.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Big data and other challenges in the quest for orthologs.Bioinformatics (Oxford, England) · 2014Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studies. Yet, while dependent on model assumptions, simulation-based benchmarking offers unique advantages: contrary to empirical data, all aspects of simulated data are known with certainty. Furthermore, the flexibility of simulation makes it possible to investigate performance factors in isolation of one another.Here, we use simulated data to dissect the performance of six methods for orthology inference available as standalone software packages (Inparanoid, OMA, OrthoInspector, OrthoMCL, QuartetS, SPIMAP) as well as two generic approaches (bidirectional best hit and reciprocal smallest distance). We investigate the impact of various evolutionary forces (gene duplication, insertion, deletion, and lateral gene transfer) and technological artefacts (ambiguous sequences) on orthology inference. We show that while gene duplication/loss and insertion/deletion are well handled by most methods (albeit for different trade-offs of precision and recall), lateral gene transfer disrupts all methods. As for ambiguous sequences, which might result from poor sequencing, assembly, or genome annotation, we show that they affect alignment score-based orthology methods more strongly than their distance-based counterparts.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.