ArticleF1000Research2020
Identifying orthologs with OMA: A primer.
Article in F1000Research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 54 citations in OpenAlex.
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila.bioRxiv : the preprint server for biology · 2026Article
- UNITe: exploiting conserved links between oncogenesis and homeostasis to identify novel cancer drivers.Frontiers in oncology · 2026Article
- OMAnnotator: a novel approach to building an annotated consensus genome sequence.Bioinformatics advances · 2026Article
- OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.Journal of molecular evolution · 2025Article
- In Vivo Models of Cardiovascular Disease:Biomedicines · 2025Review
- EdgeHOG: a method for fine-grained ancestral gene order inference at large scale.Nature ecology & evolution · 2025Article
- Feature Architecture-Aware Ortholog Search With fDOG Reveals the Distribution of Plant Cell Wall-Degrading Enzymes Across Life.Molecular biology and evolution · 2025Article
- Orthology inference at scale with FastOMA.Nature methods · 2025Article
- Most genetic roots of fungal and animal aging are hundreds of millions of years old according to phylostratigraphy analyses of aging networks.GeroScience · 2024Article
- Wild Patagonian yeast improve the evolutionary potential of novel interspecific hybrid strains for lager brewing.PLoS genetics · 2024Article
- Natural transaminase fusions for biocatalysis.RSC advances · 2024Article
- Protein-Coding Gene Families in Prokaryote Genome Comparisons.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture.G3 (Bethesda, Md.) · 2023Article
- Use ofHeliyon · 2023Article
- DrosOMA: theF1000Research · 2023Article
- Missense Variants Reveal Functional Insights Into the Human ARID Family of Gene Regulators.Journal of molecular biology · 2022Article
- PSINDB: the postsynaptic protein-protein interaction database.Database : the journal of biological databases and curation · 2022Article
- Structural and functional analysis of CCT family genes in pigeonpea.Molecular biology reports · 2022Article
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Orthologous Matrix (OMA) is a method and database that allows users to identify orthologs among many genomes. OMA provides three different types of orthologs: pairwise orthologs, OMA Groups and Hierarchical Orthologous Groups (HOGs). This Primer is organized in two parts. In the first part, we provide all the necessary background information to understand the concepts of orthology, how we infer them and the different subtypes of orthology in OMA, as well as what types of analyses they should be used for. In the second part, we describe protocols for using the OMA browser to find a specific gene and its various types of orthologs. By the end of the Primer, readers should be able to (i) understand homology and the different types of orthologs reported in OMA, (ii) understand the best type of orthologs to use for a particular analysis; (iii) find particular genes of interest in the OMA browser; and (iv) identify orthologs for a given gene. The data can be freely accessed from the OMA browser at https://omabrowser.org.
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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.