ArticleBMC bioinformatics2019
Domainoid: domain-oriented orthology inference.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms.Molecular systems biology · 2026Article
- LSGFA: domain-based infraspecific large-scale prokaryotic genomic orthologous gene inference.BMC bioinformatics · 2026Article
- DIOPT: the DRSC Integrative Ortholog Prediction Tool, 2026 update.bioRxiv : the preprint server for biology · 2026Article
- eggNOG v7: phylogeny-based orthology predictions and functional annotations.Nucleic acids research · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- A Multi-level Perspective on the Evolution of Orthologs and Their Functions.Journal of molecular evolution · 2025Review
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- Orthology inference at scale with FastOMA.Nature methods · 2025Article
- New developments for the Quest for Orthologs benchmark service.NAR genomics and bioinformatics · 2024Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.Evolution letters · 2024Article
- SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.Genome biology · 2024Article
- Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events.Frontiers in bioinformatics · 2023Article
- Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network.Genome research · 2023Article
- Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.Genomics · 2022Article
- KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases.BMC bioinformatics · 2021Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- The Quest for Orthologs benchmark service and consensus calls in 2020.Nucleic acids research · 2020Article
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4 authors.
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Abstract
backgroundOrthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been shown that orthologous proteins may differ in domain architecture, creating challenges for orthology inference methods operating on full-length sequences. We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. It employs the InParanoid algorithm on single domains separately, to infer groups of orthologous domains.
resultsThis domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories. In addition to domain level analysis, protein level orthology based on the fraction of domains that are orthologous can be inferred. Domainoid orthology assignments were compared to those yielded by the conventional full-length approach InParanoid, and were validated in a standard benchmark.
conclusionsOur results show that domain-based orthology inference can reveal many orthologous relationships that are not found by full-length sequence approaches. AVAILABILITY: https://bitbucket.org/sonnhammergroup/domainoid/.
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