Orthologous MAtrix
Names
More detailed information about this field from each metasource.
Orthologous MAtrix
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
OMA
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
oma
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
Names
More detailed information about this field from each metasource.
Orthologous MAtrix
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
OMA
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
oma
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.516556
Names
More detailed information about this field from each metasource.
Orthologous MAtrix
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
OMA
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
oma
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.516556
The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface, availability of data in a wide range of formats and interfaces, and frequent update schedule of two releases per year.
Description
More detailed information about this field from each metasource.
The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size, high quality of inferences, feature-rich web interface, availability of data in a wide range of formats and interfaces, and frequent update schedule of two releases per year.
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Orthology MAtrix
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, it is one of the largest projects of its kind.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.516556
Webpage:
http://omabrowser.org/oma/about/Webpage
More detailed information about this field from each metasource.
http://omabrowser.org/oma/about/
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://www.omabrowser.org
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://omabrowser.org/oma/home/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.516556
Licence:
Name: OMA Browser LicenceLicence name
More detailed information about this field from each metasource.
OMA Browser Licence
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
More detailed information about this field from each metasource.
http://omabrowser.org/oma/license/
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
OMA 2011: orthology inference among 1000 complete genomes
PMID: 21113020
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
PMID: 25399418
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
Algorithm of OMA for large-scale orthology inference
PMID: 19055798
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
OMA Browser--exploring orthologous relations across 352 complete genomes
PMID: 17545180
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1158
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
OMA 2011: orthology inference among 1000 complete genomes
PMID: 21113020
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
PMID: 25399418
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
Algorithm of OMA for large-scale orthology inference
PMID: 19055798
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
OMA Browser--exploring orthologous relations across 352 complete genomes
PMID: 17545180
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gku1158
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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OMA 2011: orthology inference among 1000 complete genomes
PubMed citations: 115.
115 articles citing: OMA 2011: orthology inference among 1000 complete genomes
A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans. PMID:35463453
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. PMID:33174605
Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves. PMID:32357841
OrthoFinder: phylogenetic orthology inference for comparative genomics. PMID:31727128
Structural characterization of the RH1-LZI tandem of JIP3/4 highlights RH1 domains as a cytoskeletal motor-binding motif. PMID:31690808
Duplication history and molecular evolution of the rbcS multigene family in angiosperms. PMID:31498865
Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life. PMID:30963927
Synthetic lethality guiding selection of drug combinations in ovarian cancer. PMID:30682083
Assigning confidence scores to homoeologs using fuzzy logic. PMID:30648004
Synthetic lethal combinations of low-toxicity drugs for breast cancer identified in silico by genetic screens in yeast. PMID:30555636
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications. PMID:30397019
Genomic and Transcriptomic Basis of Hanseniaspora vineae's Impact on Flavor Diversity and Wine Quality. PMID:30366992
Efficient inference of homologs in large eukaryotic pan-proteomes. PMID:30257640
Characterization of the binding mode of JNK-interacting protein 1 (JIP1) to kinesin-light chain 1 (KLC1). PMID:30026235
Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton. PMID:29914356
Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. PMID:29724166
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Early emergence of negative regulation of the tyrosine kinase Src by the C-terminal Src kinase. PMID:28939764
Constraints and consequences of the emergence of amino acid repeats in eukaryotic proteins. PMID:28805808
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. PMID:28756775
Selectivity determinants of GPCR-G-protein binding. PMID:28489817
Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships. PMID:28469416
WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PMID:27812085
Secretion-Positive LGI1 Mutations Linked to Lateral Temporal Epilepsy Impair Binding to ADAM22 and ADAM23 Receptors. PMID:27760137
Structural pliability adjacent to the kinase domain highlights contribution of FAK1 IDRs to cytoskeletal remodeling. PMID:27718363
Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma. PMID:27466804
Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach. PMID:27358369
Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction. PMID:27162151
Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny. PMID:27103098
Ensembl comparative genomics resources. PMID:26896847
SwissPalm: Protein Palmitoylation database. PMID:26339475
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. PMID:26243257
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference. PMID:26031838
Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins. PMID:25927823
Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants. PMID:25887590
YOC, A new strategy for pairwise alignment of collinear genomes. PMID:25885358
Characterization of the kidney transcriptome of the long-haired mouse Abrothrix hirta (Rodentia, Sigmodontinae) and comparison with that of the olive mouse A. olivacea. PMID:25860131
MadR1, a Mycobacterium tuberculosis cell cycle stress response protein that is a member of a widely conserved protein class of prokaryotic, eukaryotic and archeal origin. PMID:25829286
Plastid establishment did not require a chlamydial partner. PMID:25758953
Innate immune response to Streptococcus pyogenes depends on the combined activation of TLR13 and TLR2. PMID:25756897
Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal. PMID:25716788
Rock, paper, scissors: harnessing complementarity in ortholog detection methods improves comparative genomic inference. PMID:25711833
Evolution of p53 transactivation specificity through the lens of a yeast-based functional assay. PMID:25668429
A meta-approach for improving the prediction and the functional annotation of ortholog groups. PMID:25573073
Overlapping genes: a new strategy of thermophilic stress tolerance in prokaryotes. PMID:25503326
Roles for both FtsA and the FtsBLQ subcomplex in FtsN-stimulated cell constriction in Escherichia coli. PMID:25496160
Hydroxycinnamic Acid Degradation, a Broadly Conserved Trait, Protects Ralstonia solanacearum from Chemical Plant Defenses and Contributes to Root Colonization and Virulence. PMID:25423265
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. PMID:25402615
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. PMID:25398900
Text mining in cancer gene and pathway prioritization. PMID:25392685
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
Genenames.org: the HGNC resources in 2015. PMID:25361968
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PMID:25320677
Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. PMID:25158799
Orthology detection combining clustering and synteny for very large datasets. PMID:25137074
An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PMID:25111155
Big data and other challenges in the quest for orthologs. PMID:25064571
Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. PMID:24929830
Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea. PMID:24909751
The putative HORMA domain protein Atg101 dimerizes and is required for starvation-induced and selective autophagy in Drosophila. PMID:24895579
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
Studying tumorigenesis through network evolution and somatic mutational perturbations in the cancer interactome. PMID:24881052
Protein flexibility facilitates quaternary structure assembly and evolution. PMID:24866000
Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions. PMID:24865611
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. PMID:24792157
Why human disease-associated residues appear as the wild-type in other species: genome-scale structural evidence for the compensation hypothesis. PMID:24723421
eggNOG v4.0: nested orthology inference across 3686 organisms. PMID:24297252
Protein Ontology: a controlled structured network of protein entities. PMID:24270789
MetaRef: a pan-genomic database for comparative and community microbial genomics. PMID:24203705
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. PMID:24196194
TreeFam v9: a new website, more species and orthology-on-the-fly. PMID:24194607
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. PMID:24165881
Global regulatory architecture of human, mouse and rat tissue transcriptomes. PMID:24138449
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. PMID:24096415
WormBase: Annotating many nematode genomes. PMID:24058818
Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals. PMID:24013106
Shared protein complex subunits contribute to explaining disrupted co-occurrence. PMID:23874172
A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology. PMID:23865555
A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations. PMID:23819456
Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database. PMID:23815411
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. PMID:23685612
The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study. PMID:23451112
CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. PMID:23436912
Inferring hierarchical orthologous groups from orthologous gene pairs. PMID:23342000
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. PMID:23193276
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. PMID:23118485
Weak 5'-mRNA secondary structures in short eukaryotic genes. PMID:23034215
Coevolution reveals a network of human proteins originating with multicellularity. PMID:22977115
XatA, an AT-1 autotransporter important for the virulence of Xylella fastidiosa Temecula1. PMID:22950010
In vivo-validated essential genes identified in Acinetobacter baumannii by using human ascites overlap poorly with essential genes detected on laboratory media. PMID:22911967
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. PMID:22808943
Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. PMID:22799003
Surprising results on phylogenetic tree building methods based on molecular sequences. PMID:22738078
QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence. PMID:22726705
Fast and robust multiple sequence alignment with phylogeny-aware gap placement. PMID:22694311
Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. PMID:22617957
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PMID:22615551
BRCT domains: A little more than kin, and less than kind. PMID:22584059
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
Identification of ZapD as a cell division factor that promotes the assembly of FtsZ in Escherichia coli. PMID:22505682
Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes. PMID:22152004
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. PMID:22096231
The MetJ regulon in gammaproteobacteria determined by comparative genomics methods. PMID:22082356
WormBase 2012: more genomes, more data, new website. PMID:22067452
InterEvol database: exploring the structure and evolution of protein complex interfaces. PMID:22053089
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. PMID:21737420
Telling the whole story in a 10,000-genome world. PMID:21714939
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). PMID:21712341
Computational methods for Gene Orthology inference. PMID:21690100
A new, fast algorithm for detecting protein coevolution using maximum compatible cliques. PMID:21672226 -
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
PubMed citations: 111.
111 articles citing: The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback. PMID:35594844
Superoxide Initiates the Hyphal Differentiation to Microsclerotia Formation of Macrophomina phaseolina. PMID:35080446
ConVarT: a search engine for matching human genetic variants with variants from non-human species. PMID:34718716
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
Gene Erosion Can Lead to Gain-of-Function Alleles That Contribute to Bacterial Fitness. PMID:34225482
Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs. PMID:33871639
PRMT3 interacts with ALDH1A1 and regulates gene-expression by inhibiting retinoic acid signaling. PMID:33495566
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. PMID:33174605
Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species. PMID:32969558
Convergent molecular evolution among ash species resistant to the emerald ash borer. PMID:32451426
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
A multidimensional systems biology analysis of cellular senescence in aging and disease. PMID:32264951
A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PMID:32236097
Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors. PMID:31675498
Data for positive selection test and co-evolutionary analysis on mammalian cereblon. PMID:31667262
Domainoid: domain-oriented orthology inference. PMID:31660857
Duplicate divergence of two bacterial small heat shock proteins reduces the demand for Hsp70 in refolding of substrates. PMID:31652260
Reconciling event-labeled gene trees with MUL-trees and species networks. PMID:31410552
Cross-species functional modules link proteostasis to human normal aging. PMID:31269015
OMA standalone: orthology inference among public and custom genomes and transcriptomes. PMID:31235654
A web-based tool for the prediction of rice transcription factor function. PMID:31169887
Comparing time series transcriptome data between plants using a network module finding algorithm. PMID:31164912
Salmonella Typhi, Paratyphi A, Enteritidis and Typhimurium core proteomes reveal differentially expressed proteins linked to the cell surface and pathogenicity. PMID:31125353
Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. PMID:31060495
FGMP: assessing fungal genome completeness. PMID:30987585
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
Circular RNAs in human and vertebrate neural retinas. PMID:30874468
MultiDomainBenchmark: a multi-domain query and subject database suite. PMID:30764761
The Evolutionary Traceability of a Protein. PMID:30649284
Assigning confidence scores to homoeologs using fuzzy logic. PMID:30648004
Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? PMID:30496401
Automated selection of homologs to track the evolutionary history of proteins. PMID:30453878
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications. PMID:30397019
An Effective Pipeline Based on Relative Coverage for the Genome Assembly of Phytoplasmas and Other Fastidious Prokaryotes. PMID:30258279
Evolution of Olfactory Functions on the Fire Ant Social Chromosome. PMID:30239696
Insights into Kinesin-1 Activation from the Crystal Structure of KLC2 Bound to JIP3. PMID:30197037
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. PMID:30184069
JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm. PMID:30084941
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. PMID:30016513
A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process. PMID:29921904
Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m6A Modification. PMID:29730206
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss. PMID:29608732
Time-consistent reconciliation maps and forbidden time travel. PMID:29441122
Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation. PMID:29389943
The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees. PMID:29304093
Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews. PMID:29166857
Synima: a Synteny imaging tool for annotated genome assemblies. PMID:29162056
OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation. PMID:29133277
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. PMID:29106550
Inter-Species Host Gene Expression Differences in Response to Human and Avian Influenza A Virus Strains. PMID:29104227
Whole-genome assembly of Babesia ovata and comparative genomics between closely related pathogens. PMID:29078748
GPCRs globally coevolved with receptor activity-modifying proteins, RAMPs. PMID:29078385
Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis. PMID:29048526
A biologist's guide to Bayesian phylogenetic analysis. PMID:28983516
Gearing up to handle the mosaic nature of life in the quest for orthologs. PMID:28968857
Microbial genome analysis: the COG approach. PMID:28968633
Crystal structures of eukaryote glycosyltransferases reveal biologically relevant enzyme homooligomers. PMID:28932871
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. PMID:28881964
The core transcriptome of mammalian placentas and the divergence of expression with placental shape. PMID:28864021
Biologically feasible gene trees, reconciliation maps and informative triples. PMID:28861118
Orthonome - a new pipeline for predicting high quality orthologue gene sets applicable to complete and draft genomes. PMID:28859620
Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates. PMID:28824604
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. PMID:28756775
Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family. PMID:28754924
Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes. PMID:28746735
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
The gene family-free median of three. PMID:28559921
Identification of innate lymphoid cells in single-cell RNA-Seq data. PMID:28534222
Differential manipulation of arrestin-3 binding to basal and agonist-activated G protein-coupled receptors. PMID:28461104
Core Genes Evolve Rapidly in the Long-Term Evolution Experiment with Escherichia coli. PMID:28379360
The RegA regulon exhibits variability in response to altered growth conditions and differs markedly between Rhodobacter species. PMID:28348828
Comparative genomics reveals contraction in olfactory receptor genes in bats. PMID:28325942
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. PMID:28209129
Tutorial on Protein Ontology Resources. PMID:28150233
Protein Bioinformatics Databases and Resources. PMID:28150231
Developing integrated crop knowledge networks to advance candidate gene discovery. PMID:28018846
An Essential Factor for High Mg2+ Tolerance of Staphylococcus aureus. PMID:27933050
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. PMID:27899649
Oral transfer of chemical cues, growth proteins and hormones in social insects. PMID:27894417
Primer on the Gene Ontology. PMID:27812933
Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes. PMID:27801289
A computational interactome and functional annotation for the human proteome. PMID:27770567
HieranoiDB: a database of orthologs inferred by Hieranoid. PMID:27742821
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PMID:27711162
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
MultiSyn: A Webtool for Multiple Synteny Detection and Visualization of User's Sequence of Interest Compared to Public Plant Species. PMID:27594782
Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life. PMID:27501943
The multiple evolutionary origins of the eukaryotic N-glycosylation pathway. PMID:27492357
Role of mRNA structure in the control of protein folding. PMID:27466388
Computational Identification of the Paralogs and Orthologs of Human Cytochrome P450 Superfamily and the Implication in Drug Discovery. PMID:27367670
AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana. PMID:27338257
Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics. PMID:27312960
The Response Regulator BfmR Is a Potential Drug Target for Acinetobacter baumannii. PMID:27303741
Towards Consensus Gene Ages. PMID:27259914
The Orthology Ontology: development and applications. PMID:27259657
Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web. PMID:27189561
Standardized benchmarking in the quest for orthologs. PMID:27043882
Homoeologs: What Are They and How Do We Infer Them? PMID:27021699
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. PMID:26980519
Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. PMID:26774999
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Iron-Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein-Protein Interaction. PMID:26545917
Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli. PMID:26537891
Prediction of microbial phenotypes based on comparative genomics. PMID:26451672
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site. PMID:26447800
Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes. PMID:25927816
Characterization and structure prediction of partial length protein sequences of pcoA, pcoR and chrB genes from heavy metal resistant bacteria from the Klip River, South Africa. PMID:25837632
The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. PMID:25593347 -
Algorithm of OMA for large-scale orthology inference
PubMed citations: 83.
83 articles citing: Algorithm of OMA for large-scale orthology inference
The Quest for Orthologs orthology benchmark service in 2022. PMID:35552456
Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes. PMID:34971383
Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs. PMID:33871639
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs. PMID:33606106
The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle. PMID:32973093
CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets. PMID:32886787
Reconstruction of time-consistent species trees. PMID:32843891
Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves. PMID:32357841
Identifying orthologs with OMA: A primer. PMID:32089838
Primary orthologs from local sequence context. PMID:32028880
Best match graphs and reconciliation of gene trees with species trees. PMID:32002659
Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. PMID:31827597
Phylogenomics provides robust support for a two-domains tree of life. PMID:31819234
SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. PMID:31648300
Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling. PMID:31270537
OMA standalone: orthology inference among public and custom genomes and transcriptomes. PMID:31235654
Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. PMID:31127117
Assigning confidence scores to homoeologs using fuzzy logic. PMID:30648004
Immune genes are hotspots of shared positive selection across birds and mammals. PMID:30620335
Amphioxus functional genomics and the origins of vertebrate gene regulation. PMID:30464347
Efficient inference of homologs in large eukaryotic pan-proteomes. PMID:30257640
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. PMID:30120140
TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. PMID:30049970
Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa. PMID:30034216
Accurate prediction of orthologs in the presence of divergence after duplication. PMID:29950018
Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution. PMID:29490679
Time-consistent reconciliation maps and forbidden time travel. PMID:29441122
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. PMID:28881964
Integrative modeling of gene and genome evolution roots the archaeal tree of life. PMID:28533395
Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach. PMID:28261179
The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation. PMID:27821409
Phylogenomics and Divergence Dating of Fungus-Farming Ants (Hymenoptera: Formicidae) of the Genera Sericomyrmex and Apterostigma. PMID:27466804
Homoeologs: What Are They and How Do We Infer Them? PMID:27021699
Inferring Orthologs: Open Questions and Perspectives. PMID:26966373
Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes. PMID:26927182
An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species. PMID:26605337
Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity. PMID:25888333
Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation. PMID:25764302
Phylogenetic profiling: how much input data is enough? PMID:25679783
A phylogenetic backbone for Bivalvia: an RNA-seq approach. PMID:25589608
What helminth genomes have taught us about parasite evolution. PMID:25482650
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. PMID:25428351
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology. PMID:25320677
Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. PMID:25158799
Reconciliation of gene and species trees. PMID:24800245
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. PMID:24580726
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. PMID:24096415
Shared protein complex subunits contribute to explaining disrupted co-occurrence. PMID:23874172
A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology. PMID:23865555
How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome. PMID:23840335
AliquotG: an improved heuristic algorithm for genome aliquoting. PMID:23691189
Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl. PMID:23631913
The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study. PMID:23451112
Inferring hierarchical orthologous groups from orthologous gene pairs. PMID:23342000
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information. PMID:23248024
The evolution of ultraconserved elements with different phylogenetic origins. PMID:23217155
BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity. PMID:23046607
Gene copy number variation and its significance in cyanobacterial phylogeny. PMID:22894826
Surprising results on phylogenetic tree building methods based on molecular sequences. PMID:22738078
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PMID:22615551
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations. PMID:22563391
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PMID:22174796
ALF--a simulation framework for genome evolution. PMID:22160766
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). PMID:21712341
Computational methods for Gene Orthology inference. PMID:21690100
QuartetS: a fast and accurate algorithm for large-scale orthology detection. PMID:21572104
iPhy: an integrated phylogenetic workbench for supermatrix analyses. PMID:21261969
OrthoInspector: comprehensive orthology analysis and visual exploration. PMID:21219603
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. PMID:21149299
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
Orthology confers intron position conservation. PMID:20598118
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. PMID:20439257
The obesity gene, TMEM18, is of ancient origin, found in majority of neuronal cells in all major brain regions and associated with obesity in severely obese children. PMID:20380707
Phylogenetic assessment of alignments reveals neglected tree signal in gaps. PMID:20370897
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
Joining forces in the quest for orthologs. PMID:19785718
HaMStR: profile hidden markov model based search for orthologs in ESTs. PMID:19586527
The Microbe browser for comparative genomics. PMID:19406928
Phylogenetic and functional assessment of orthologs inference projects and methods. PMID:19148271 -
OMA Browser--exploring orthologous relations across 352 complete genomes
PubMed citations: 62.
62 articles citing: OMA Browser--exploring orthologous relations across 352 complete genomes
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
Identification of Rare LRP5 Variants in a Cohort of Males with Impaired Bone Mass. PMID:34639175
The pVHL neglected functions, a tale of hypoxia-dependent and -independent regulations in cancer. PMID:32603638
Systematic prediction of FFAT motifs across eukaryote proteomes identifies nucleolar and eisosome proteins with the predicted capacity to form bridges to the endoplasmic reticulum. PMID:31777772
Characterization of intellectual disability and autism comorbidity through gene panel sequencing. PMID:31209962
The clinical spectrum of CASQ1-related myopathy. PMID:30258016
Exploring the mechanistic insights of Cas scaffolding protein family member 4 with protein tyrosine kinase 2 in Alzheimer's disease by evaluating protein interactions through molecular docking and dynamic simulations. PMID:29789968
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. PMID:29751792
The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees. PMID:29304093
Structural complexity and functional diversity of plant NADPH oxidases. PMID:29071531
Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. PMID:26782935
Computational analysis of prolyl hydroxylase domain-containing protein 2 (PHD2) mutations promoting polycythemia insurgence in humans. PMID:26754054
Are Synonymous Sites in Primates and Rodents Functionally Constrained? PMID:26563252
Isoform-specific interactions of the von Hippel-Lindau tumor suppressor protein. PMID:26211615
Multi-walled carbon nanotube-induced gene expression in vitro: concordance with in vivo studies. PMID:25511174
Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. PMID:25217615
Orthology detection combining clustering and synteny for very large datasets. PMID:25137074
Coevolution signals capture the specific packing of secondary structures in protein architecture. PMID:24699983
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. PMID:24684742
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
Predicting protein-protein interaction by the mirrortree method: possibilities and limitations. PMID:24349035
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. PMID:24196194
Global regulatory architecture of human, mouse and rat tissue transcriptomes. PMID:24138449
GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. PMID:24096415
How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome. PMID:23840335
Complementing the Eukaryotic Protein Interactome. PMID:23825550
A semi-automated genome annotation comparison and integration scheme. PMID:23725374
The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition. PMID:23661679
Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales. PMID:23408961
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
Investigating the Relationship between Topology and Evolution in a Dynamic Nematode Odor Genetic Network. PMID:23056995
BBH-LS: an algorithm for computing positional homologs using sequence and gene context similarity. PMID:23046607
Protein-protein-interaction network organization of the hypusine modification system. PMID:22888148
Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations. PMID:22563391
Roundup 2.0: enabling comparative genomics for over 1800 genomes. PMID:22247275
Identifying single copy orthologs in Metazoa. PMID:22144877
Developing a community-based genetic nomenclature for anole lizards. PMID:22077994
Structural requirements for interaction of peroxisomal targeting signal 2 and its receptor PEX7. PMID:22057399
An integrative approach to ortholog prediction for disease-focused and other functional studies. PMID:21880147
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
Markov models of amino acid substitution to study proteins with intrinsically disordered regions. PMID:21647374
Proteinortho: detection of (co-)orthologs in large-scale analysis. PMID:21526987
Identification of drought-responsive universal stress proteins in viridiplantae. PMID:21423406
Bacterial protein structures reveal phylum dependent divergence. PMID:21315656
Searching the protein structure database for ligand-binding site similarities using CPASS v.2. PMID:21269480
IsoBase: a database of functionally related proteins across PPI networks. PMID:21177658
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. PMID:21149299
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2. PMID:20863412
F-BAR domain proteins: Families and function. PMID:20585502
Empirical analysis of the most relevant parameters of codon substitution models. PMID:20526712
Getting started in gene orthology and functional analysis. PMID:20361041
Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. PMID:20333182
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. PMID:20003425
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity. PMID:19906735
ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses. PMID:19846609
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. PMID:19698106
The Chicken Gene Nomenclature Committee report. PMID:19607656
Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. PMID:19521530
Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships. PMID:19467333
Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. PMID:19105848
Algorithm of OMA for large-scale orthology inference. PMID:19055798 - http://dx.doi.org/10.1093/nar/gku1158
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orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
evolutionary biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
comparative genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556
Tags
More detailed information about this field from each metasource.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: OMA; Orthologous MAtrix; DOI: https://doi.org/10.25504/FAIRsharing.g3j5qj; Last edited: Jan. 8, 2019, 1:24 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
evolutionary biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.516556
comparative genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.516556
orthology protein sequence protein domains and classification evolutionary biology comparative genomics
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