HOGENOM
Names
More detailed information about this field from each metasource.
HOGENOM
metasource: Fairsharing.org
version: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
hogenom
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Names
More detailed information about this field from each metasource.
HOGENOM
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
hogenom
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Names
More detailed information about this field from each metasource.
HOGENOM
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
hogenom
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.
Description
More detailed information about this field from each metasource.
HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
It allows selection of sets of homologous genes among species, and visualisation of multiple alignments and phylogenetic trees. It is useful for comparative sequence analysis, phylogeny, molecular evolution studies and to get a view of what is known about a peculiar gene family.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Webpage:
http://hogenom.univ-lyon1.fr/Webpage
More detailed information about this field from each metasource.
http://hogenom.univ-lyon1.fr/
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://pbil.univ-lyon1.fr/databases/hogenom3.html
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Licence:
Name: CeCILL licenseLicence name
More detailed information about this field from each metasource.
CeCILL license
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Licence URL
More detailed information about this field from each metasource.
https://cecill.info/licences.fr.html
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Databases of homologous gene families for comparative genomics
PMID: 19534752
metasource: Fairsharing.org
version: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1186/1471-2105-10-S6-S3
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Publications
More detailed information about this field from each metasource.
Databases of homologous gene families for comparative genomics
PMID: 19534752
metasource: Fairsharing.org
version: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1186/1471-2105-10-S6-S3
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
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Databases of homologous gene families for comparative genomics
PubMed citations: 71.
71 articles citing: Databases of homologous gene families for comparative genomics
A Pan-Cancer Analysis of the Oncogenic Role of WD Repeat Domain 74 in Multiple Tumors. PMID:35559034
The Structural Determinants of Intra-Protein Compensatory Substitutions. PMID:35349721
Relative Time Constraints Improve Molecular Dating. PMID:34668564
RapGreen, an interactive software and web package to explore and analyze phylogenetic trees. PMID:34568824
Combining transposon mutagenesis and reporter genes to identify novel regulators of the topA promoter in Streptomyces. PMID:33985526
An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. PMID:32899740
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss. PMID:32502238
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. PMID:32343307
Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes? PMID:30917603
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
Roles of the DedD Protein in Escherichia coli Cell Constriction. PMID:30692172
CAARS: comparative assembly and annotation of RNA-Seq data. PMID:30452539
GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution. PMID:29764363
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. PMID:29220487
Ancient genes establish stress-induced mutation as a hallmark of cancer. PMID:28441401
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies. PMID:28402423
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
A computational interactome and functional annotation for the human proteome. PMID:27770567
LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. PMID:27702814
Efficient Gene Tree Correction Guided by Genome Evolution. PMID:27513924
SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage. PMID:27401173
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation. PMID:27190002
The link between orthology relations and gene trees: a correction perspective. PMID:27087831
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. PMID:26903996
A generalized birth and death process for modeling the fates of gene duplication. PMID:26643106
Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins. PMID:26604664
Reconstructing a SuperGeneTree minimizing reconciliation. PMID:26451911
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. PMID:26450112
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. PMID:26323765
Plastid establishment did not require a chlamydial partner. PMID:25758953
Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts. PMID:25714744
GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands. PMID:25659072
Joint amalgamation of most parsimonious reconciled gene trees. PMID:25380957
Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees. PMID:25371435
Reductive genome evolution at both ends of the bacterial population size spectrum. PMID:25220308
Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. PMID:24398320
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. PMID:24275491
Reconciliation-based detection of co-evolving gene families. PMID:24252193
Efficient exploration of the space of reconciled gene trees. PMID:23925510
EGN: a wizard for construction of gene and genome similarity networks. PMID:23841456
Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26. PMID:23589360
Reconciliation and local gene tree rearrangement can be of mutual profit. PMID:23566548
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. PMID:23558341
Ndufaf5 deficiency in the Dictyostelium model: new roles in autophagy and development. PMID:23536703
TPMS: a set of utilities for querying collections of gene trees. PMID:23530580
Lateral gene transfer from the dead. PMID:23355531
Evolution of coding microsatellites in primate genomes. PMID:23315383
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. PMID:23203876
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
Detection of bacterial 16S rRNA and identification of four clinically important bacteria by real-time PCR. PMID:23139793
Genome-scale coestimation of species and gene trees. PMID:23132911
The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain. PMID:23107454
Computational workflow for analysis of gain and loss of genes in distantly related genomes. PMID:23046496
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. PMID:23043116
Weak 5'-mRNA secondary structures in short eukaryotic genes. PMID:23034215
The chordate proteome history database. PMID:22904610
Evidence for widespread GC-biased gene conversion in eukaryotes. PMID:22628461
Lateral gene transfer as a support for the tree of life. PMID:22416123
Identification and characterization of a bacterial hydrosulphide ion channel. PMID:22407320
Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PMID:22174796
Wdr74 is required for blastocyst formation in the mouse. PMID:21799883
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. PMID:21737420
The two tryptophans of β2-microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure. PMID:21663612
Ultra-fast sequence clustering from similarity networks with SiLiX. PMID:21513511
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
PhEVER: a database for the global exploration of virus-host evolutionary relationships. PMID:21081560
An efficient method to find potentially universal population genetic markers, applied to metazoans. PMID:20836842
Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. PMID:20551039
The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community. PMID:19534734 - http://dx.doi.org/10.1186/1471-2105-10-S6-S3
Tags:
Tags
More detailed information about this field from each metasource.
classification
metasource: Fairsharing.org
version: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
homologous
metasource: Fairsharing.org
version: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
region
metasource: Fairsharing.org
version: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
gene and protein families
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.
classification
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
homologous
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
region
metasource: Fairsharing.orgversion: FAIRsharing.org: HOGENOM; HOGENOM; DOI: https://doi.org/10.25504/FAIRsharing.qe8tz8; Last edited: Sept. 24, 2020, 2:23 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
sequence analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
gene and protein families
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
classification homologous orthology region sequence analysis gene and protein families phylogenetics comparative genomics phylogenomics
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