Chlamydiae Database
Abbreviation:ChlamDB
General Information
ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using accessions numbers of the most widely used databases including COG, KEGG ortholog, KEGG pathway, KEGG module, Pfam and InterPro. Candidate effectors of the Type III secretion system (T3SS) were identified using four in silico methods. The identification of orthologs among all PVC genomes allows users to perform large-scale comparative analyses and to identify orthologs of any protein in all genomes integrated in the database. Phylogenetic relationships of PVC proteins and their closest homologs in RefSeq, comparison of transmembrane domains and Pfam domains, conservation of gene neighborhood and taxonomic profiles can be visualized using dynamically generated graphs, available for download. As a central resource for researchers working on chlamydia, chlamydia-related bacteria, verrucomicrobia and planctomyces, ChlamDB facilitates the access to comprehensive annotations and integrates multiple tools for comparative genomic analyses.
How to cite this record
FAIRsharing.org: ChlamDB; Chlamydiae Database; DOI: https://doi.org/10.25504/FAIRsharing.rgcsW6;
Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Apr 11 2021 1:28 p.m.
Publication for citation
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum.
Pillonel T,Tagini F,Bertelli C,Greub G; Nucleic Acids Res ;
2019;
gkz924;
Record added: Nov. 1, 2019, 10:09 a.m.
Record updated:
Nov. 1, 2019, 9:35 p.m. by The FAIRsharing Team.
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Edits to 'https://fairsharing.org/FAIRsharing.rgcsW6' by 'The FAIRsharing Team' at 21:35, 01 Nov 2019 (approved):
'organizations' has been modified:
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Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Switzerland|https://www.chuv.ch/en/microbiologie/imu-home/research/research-groups/gilbert-greub/|Undefined
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Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Switzerland|https://www.chuv.ch/en/microbiologie/imu-home/research/research-groups/gilbert-greub/|Maintains
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Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Switzerland|https://www.chuv.ch/en/microbiologie/imu-home/research/research-groups/gilbert-greub/|Maintains
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Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Switzerland|https://www.chuv.ch/en/microbiologie/imu-home/research/research-groups/gilbert-greub/|Undefined
'related_databases' has been modified:
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Pfam
STRING
Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
Reference Sequence Database
Transporter Classification Database
PRofils pour l'Identification Automatique du Metabolisme
UniProt Knowledgebase
Kyoto Encyclopedia of Genes and Genomes
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Pfam
STRING
Clusters of Orthologous Groups of Proteins: Phylogenetic classification of proteins encoded in complete genomes
Reference Sequence Database
Transporter Classification Database
PRofils pour l'Identification Automatique du Metabolisme
UniProt Knowledgebase
Kyoto Encyclopedia of Genes and Genomes
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'supportLinks' has been modified:
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help|https://github.com/metagenlab/chlamdb/issues
online documentation|https://chlamdb.ch/docs/index.html
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help|https://github.com/metagenlab/chlamdb/issues
online documentation|https://chlamdb.ch/docs/index.html
online documentation|https://chlamdb.ch/about
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online documentation|https://chlamdb.ch/about
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'onto_disciplines' has been modified:
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Comparative Genomics
Phylogenomics
Phylogeny
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Comparative Genomics
Phylogenomics
Phylogeny
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'dataProcesses' has been modified:
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Sequence search
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Extract Genomic Region
Extract Orthogroups
Extract COGs
Extract Pfam Domains
Extract InterPro Entries
Extract KEGG Orthologs
TCDB Annotation Search
View KEGG Maps
View KEGG Modules
Added:
Extract Genomic Region
Extract Orthogroups
Extract COGs
Extract Pfam Domains
Extract InterPro Entries
Extract KEGG Orthologs
TCDB Annotation Search
View KEGG Maps
View KEGG Modules
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Sequence search
'onto_domains' has been modified:
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Protein domain
conserved_region
genome
homologous
orthologous
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Protein domain
conserved_region
genome
homologous
orthologous
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'tools' has been modified:
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BLAST||https://chlamdb.ch/blast/
Plot Genomic Region||https://chlamdb.ch/plot_region/
Circos Plots||https://chlamdb.ch/circos/
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BLAST||https://chlamdb.ch/blast/
Plot Genomic Region||https://chlamdb.ch/plot_region/
Circos Plots||https://chlamdb.ch/circos/
Removed:
Access / Retrieve Data
Conditions of Use
Data Access
Publications
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum.
Pillonel T,Tagini F,Bertelli C,Greub G
Nucleic Acids Res 2019
View Paper (PubMed)
View Publication
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