ArticleNucleic acids research2015
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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129 citing papers in PubMed, 223 citations in OpenAlex.
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- Comparative structural and functional analysis of the glycine-rich regions of Class A and B J-domain protein cochaperones of Hsp70.FEBS letters · 2024Article
- OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.Nucleic acids research · 2024Article
- Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.Nature biotechnology · 2024Article
- Chromosome-level genome assembly of Babesia caballi reveals diversity of multigene families among Babesia species.BMC genomics · 2023Article
- Protein length distribution is remarkably uniform across the tree of life.Genome biology · 2023Article
- Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in Epiperipatus broadwayi.Genome biology and evolution · 2023Article
- Heritability and gene functions associated with sclerotia formation ofMicrobial genomics · 2023Article
- Analysis of Pneumocystis Transcription Factor Evolution and Implications for Biology and Lifestyle.mBio · 2023Article
- Plant-PathogenicmBio · 2023Article
- Mutant structure of metabolic switch protein in complex with monomeric c-di-GMP reveals a potential mechanism of protein-mediated ligand dimerization.Scientific reports · 2023Article
- Whole genome sequence and diversity in multigene families ofFrontiers in cellular and infection microbiology · 2023Article
- Defining the extent of gene function using ROC curvature.Bioinformatics (Oxford, England) · 2022Article
- Read2Tree: scalable and accurate phylogenetic trees from raw reads.bioRxiv : the preprint server for biology · 2022Article
- Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants.International journal of molecular sciences · 2022Review
- Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback.Genome biology and evolution · 2022Article
- Superoxide Initiates the Hyphal Differentiation to Microsclerotia Formation ofMicrobiology spectrum · 2022Article
- ConVarT: a search engine for matching human genetic variants with variants from non-human species.Nucleic acids research · 2022Article
69 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 5 institutions in 4 countries.
Funding
Abstract
The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://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.