GreenPhylDB: A phylogenomic database for plant comparative genomics
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GreenPhylDB: A phylogenomic database for plant comparative genomics
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GreenPhyl
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GreenPhylDB
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
greenphyldb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
Names
More detailed information about this field from each metasource.
GreenPhylDB: A phylogenomic database for plant comparative genomics
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GreenPhyl
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GreenPhylDB
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
greenphyldb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
Other names: GreenPhyl, GreenPhylDB, greenphyldb
Names
More detailed information about this field from each metasource.
GreenPhylDB: A phylogenomic database for plant comparative genomics
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GreenPhyl
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GreenPhylDB
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
greenphyldb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
This source may no longer be available. No known URL could be resolved successfully.
GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.
Description
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GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GreenPhylDB is a web resource designed for comparative and functional genomics in plants. The database contains a catalogue of gene families based on gene predictions of genomes, covering a broad taxonomy of green plants. Result of our automatic clustering is manually annotated and analyzed by a phylogenetic-based approach to predict homologous relationships. It supports evolution and functional studies to identify candidate gene affecting agronomic traits in crops.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
A database designed for comparative and functional genomics based on complete genomes. It contains full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
Webpage:
http://www.greenphyl.orgWebpage
More detailed information about this field from each metasource.
http://www.greenphyl.org
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
https://v5.greenphyl.org
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://www.greenphyl.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
Licence:
Name: GreenPhyl Terms of ServiceLicence name
More detailed information about this field from each metasource.
GreenPhyl Terms of Service
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
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http://www.greenphyl.org/cgi-bin/tos.cgi
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
GreenPhylDB v2.0: comparative and functional genomics in plants
PMID: 20864446
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
https://doi.org/10.1093/nar/gkaa1068
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkm934
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
Publications
More detailed information about this field from each metasource.
GreenPhylDB v2.0: comparative and functional genomics in plants
PMID: 20864446
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
https://doi.org/10.1093/nar/gkaa1068
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkm934
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
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GreenPhylDB v2.0: comparative and functional genomics in plants
PubMed citations: 57.
57 articles citing: GreenPhylDB v2.0: comparative and functional genomics in plants
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
GreenPhylDB v5: a comparative pangenomic database for plant genomes. PMID:33237299
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Glycosyltransferase Family 61 in Liliopsida (Monocot): The Story of a Gene Family Expansion. PMID:30619412
Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine. PMID:30497367
Three New Genome Assemblies Support a Rapid Radiation in Musa acuminata (Wild Banana). PMID:30321324
MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. PMID:29220435
A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.). PMID:29166879
Diversification of Root Hair Development Genes in Vascular Plants. PMID:28487476
Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships. PMID:28469416
New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. PMID:28424707
Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. PMID:28368449
Evolutionary Analyses of GRAS Transcription Factors in Angiosperms. PMID:28303145
Computational Tools for Genomic Studies in Plants. PMID:28217007
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
Lineage-Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening. PMID:27994606
Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants. PMID:27760122
A Systematic View of the MLO Family in Rice Suggests Their Novel Roles in Morphological Development, Diurnal Responses, the Light-Signaling Pathway, and Various Stress Responses. PMID:27729915
Bioinformatics Approach in Plant Genomic Research. PMID:27499685
SpinachDB: A Well-Characterized Genomic Database for Gene Family Classification and SNP Information of Spinach. PMID:27148975
A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop. PMID:27144345
Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. PMID:26935041
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform. PMID:26869702
Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. PMID:26848538
pATsi: Paralogs and Singleton Genes from Arabidopsis thaliana. PMID:26792975
Bioinformatic landscapes for plant transcription factor system research. PMID:26719053
Information Commons for Rice (IC4R). PMID:26519466
Conserved Gene Expression Programs in Developing Roots from Diverse Plants. PMID:26265761
The roots of future rice harvests. PMID:26224558
Phylogenomics databases for facilitating functional genomics in rice. PMID:26223238
Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement. PMID:25874133
GenomicusPlants: a web resource to study genome evolution in flowering plants. PMID:25432975
Proteome analysis of cytoplasmatic and plastidic β-carotene lipid droplets in Dunaliella bardawil. PMID:25404729
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
The coffee genome hub: a resource for coffee genomes. PMID:25392413
PLAZA 3.0: an access point for plant comparative genomics. PMID:25324309
Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics. PMID:25253557
Impact of recurrent gene duplication on adaptation of plant genomes. PMID:24884640
Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. PMID:24833233
From plant genomes to protein families: computational tools. PMID:24688740
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots. PMID:24570169
POGs2: a web portal to facilitate cross-species inferences about protein architecture and function in plants. PMID:24340041
MEGANTE: a web-based system for integrated plant genome annotation. PMID:24253915
Machine learning approaches distinguish multiple stress conditions using stress-responsive genes and identify candidate genes for broad resistance in rice. PMID:24235132
Genes and co-expression modules common to drought and bacterial stress responses in Arabidopsis and rice. PMID:24130868
Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress. PMID:23852542
Genome-wide expression analysis of rice aquaporin genes and development of a functional gene network mediated by aquaporin expression in roots. PMID:23801298
The banana genome hub. PMID:23707967
PGDD: a database of gene and genome duplication in plants. PMID:23180799
PIECE: a database for plant gene structure comparison and evolution. PMID:23180792
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. PMID:22801500
Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. PMID:22793791
Comparative Genomics and Molecular Characterization of the Maize PIN Family Proteins. PMID:22629275
Roundup 2.0: enabling comparative genomics for over 1800 genomes. PMID:22247275
Dissecting plant genomes with the PLAZA comparative genomics platform. PMID:22198273
Identification and characterization of NF-Y transcription factor families in the monocot model plant Brachypodium distachyon. PMID:21738795 - https://doi.org/10.1093/nar/gkaa1068
- http://dx.doi.org/10.1093/nar/gkm934
Tags:
Tags
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genome
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
homologous
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
sequence cluster
metasource: Fairsharing.org
version: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
arabidopsis thaliana
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
rice
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
plant biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
phylogenetics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:16.714633
Tags
More detailed information about this field from each metasource.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
homologous
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
orthologous
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
sequence cluster
metasource: Fairsharing.orgversion: FAIRsharing.org: GreenPhyl; GreenPhylDB: A phylogenomic database for plant comparative genomics; DOI: https://doi.org/10.25504/FAIRsharing.j98570; Last edited: April 26, 2021, 8:43 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
plant databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
arabidopsis thaliana
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
rice
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
plant biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
phylogenetics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:16.714633
genome homologous orthology sequence cluster plant rice plant biology gene and protein families phylogenetics genomics
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