Homologous Vertebrate Genes Database
Names
More detailed information about this field from each metasource.
Homologous Vertebrate Genes Database
metasource: Fairsharing.org
version: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HOVERGEN
metasource: Fairsharing.org
version: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Homologous vertebrate genes database (HOVERGEN)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
hovergen
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Names
More detailed information about this field from each metasource.
Homologous Vertebrate Genes Database
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HOVERGEN
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Homologous vertebrate genes database (HOVERGEN)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
hovergen
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Other names: HOVERGEN, Homologous vertebrate genes database (HOVERGEN), hovergen
Names
More detailed information about this field from each metasource.
Homologous Vertebrate Genes Database
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
HOVERGEN
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Homologous vertebrate genes database (HOVERGEN)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
hovergen
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.
Description
More detailed information about this field from each metasource.
HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
This database allows selection of sets of homologous genes among vertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Webpage:
http://pbil.univ-lyon1.fr/databases/hovergen.htmlWebpage
More detailed information about this field from each metasource.
http://pbil.univ-lyon1.fr/databases/hovergen.html
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Publications:
Publications
More detailed information about this field from each metasource.
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
PMID: 15713731
metasource: Fairsharing.org
version: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/bioinformatics/bti325
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Publications
More detailed information about this field from each metasource.
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
PMID: 15713731
metasource: Fairsharing.org
version: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://dx.doi.org/10.1093/bioinformatics/bti325
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
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Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
PubMed citations: 75.
75 articles citing: Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II (GBSSII) Gene in Korean Rice Accessions (KRICE_CORE). PMID:34681408
RapGreen, an interactive software and web package to explore and analyze phylogenetic trees. PMID:34568824
Inferring the Deep Past from Molecular Data. PMID:33772552
GreenPhylDB v5: a comparative pangenomic database for plant genomes. PMID:33237299
Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity. PMID:32877529
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? PMID:32714773
Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses. PMID:32194601
Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders. PMID:32183904
Best match graphs and reconciliation of gene trees with species trees. PMID:32002659
Identification of pathogenic variant enriched regions across genes and gene families. PMID:31871067
Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis. PMID:31428542
Gene tree species tree reconciliation with gene conversion. PMID:30767052
iHam and pyHam: visualizing and processing hierarchical orthologous groups. PMID:30508066
OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation. PMID:29133277
New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. PMID:28424707
Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants. PMID:28173747
Development of High Affinity and High Specificity Inhibitors of Matrix Metalloproteinase 14 through Computational Design and Directed Evolution. PMID:28087697
Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms. PMID:26773008
Transcriptional and post-transcriptional regulation of the jasmonate signalling pathway in response to abiotic and harvesting stress in Hevea brasiliensis. PMID:25443311
Sequence and expression analyses of ethylene response factors highly expressed in latex cells from Hevea brasiliensis. PMID:24971876
Family size evolution in Drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods. PMID:24951565
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
Impact of recurrent gene duplication on adaptation of plant genomes. PMID:24884640
Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots. PMID:24570169
Lipid transfer proteins in coffee: isolation of Coffea orthologs, Coffea arabica homeologs, expression during coffee fruit development and promoter analysis in transgenic tobacco plants. PMID:24469961
ITEP: an integrated toolkit for exploration of microbial pan-genomes. PMID:24387194
TPMS: a set of utilities for querying collections of gene trees. PMID:23530580
Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis. PMID:23268714
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
Genome-scale coestimation of species and gene trees. PMID:23132911
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. PMID:23088596
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. PMID:22454131
Computational methods for Gene Orthology inference. PMID:21690100
QuartetS: a fast and accurate algorithm for large-scale orthology detection. PMID:21572104
Hal: an automated pipeline for phylogenetic analyses of genomic data. PMID:21327165
Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. PMID:21320298
Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation. PMID:20920266
An efficient method to find potentially universal population genetic markers, applied to metazoans. PMID:20836842
A Bayesian approach for fast and accurate gene tree reconstruction. PMID:20660489
Deep-coverage rhesus red blood cell proteome: a first comparison with the human and mouse red blood cell. PMID:20606743
Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. PMID:20551039
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. PMID:20439257
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
Getting started in gene orthology and functional analysis. PMID:20361041
Utility of computational methods to identify the apoptosis machinery in unicellular eukaryotes. PMID:19812769
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. PMID:19765311
Databases of homologous gene families for comparative genomics. PMID:19534752
Relationship between phylogenetic distribution and genomic features in Neurospora crassa. PMID:19461939
Berkeley PHOG: PhyloFacts orthology group prediction web server. PMID:19435885
Evolution of proteins and proteomes: a phylogenetics approach. PMID:19325853
Strategies for reliable exploitation of evolutionary concepts in high throughput biology. PMID:19204813
Revisiting the missing protein-coding gene catalog of the domestic dog. PMID:19193219
Developmental constraints on vertebrate genome evolution. PMID:19096706
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. PMID:19029536
Large-scale assignment of orthology: back to phylogenetics? PMID:18983710
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. PMID:18948295
Dealing with incongruence in phylogenomic analyses. PMID:18852109
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. PMID:18834516
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. PMID:18832367
Reconciliation with non-binary species trees. PMID:18808330
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. PMID:18562677
Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation. PMID:18485197
Overlapping genes in the human and mouse genomes. PMID:18410680
TreeFam: 2008 Update. PMID:18056084
Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. PMID:18047665
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. PMID:17989260
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. PMID:17982176
primetv: a viewer for reconciled trees. PMID:17484781
Hierarchical classification of functionally equivalent genes in prokaryotes. PMID:17353185
Orthology prediction at scalable resolution by phylogenetic tree analysis. PMID:17346331
Ensembl 2007. PMID:17148474
PhyloPat: phylogenetic pattern analysis of eukaryotic genes. PMID:16948844
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. PMID:16434444
TreeFam: a curated database of phylogenetic trees of animal gene families. PMID:16381935
INVHOGEN: a database of homologous invertebrate genes. PMID:16381884 - http://dx.doi.org/10.1093/bioinformatics/bti325
Tags:
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
phylogenetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
comparative genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
phylogenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Tags
More detailed information about this field from each metasource.
deoxyribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: HOVERGEN; Homologous Vertebrate Genes Database; DOI: https://doi.org/10.25504/FAIRsharing.dg1f0e; Last edited: Jan. 8, 2019, 1:19 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
sequence analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
phylogenetics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
comparative genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
phylogenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
dna gene protein gene and protein families sequence analysis phylogenetics comparative genomics phylogenomics
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