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.
Show edit history
Hide edit history
Edits to 'https://fairsharing.org/FAIRsharing.rgcsW6' by 'The FAIRsharing Team' at 21:35, 01 Nov 2019 (approved):
'organizations' has been modified:
Before:
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
After:
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
Added:
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
Removed:
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:
Before:
After:
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
Added:
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
Removed:
'supportLinks' has been modified:
Before:
help|https://github.com/metagenlab/chlamdb/issues
online documentation|https://chlamdb.ch/docs/index.html
After:
help|https://github.com/metagenlab/chlamdb/issues
online documentation|https://chlamdb.ch/docs/index.html
online documentation|https://chlamdb.ch/about
Added:
online documentation|https://chlamdb.ch/about
Removed:
'onto_disciplines' has been modified:
Before:
After:
Comparative Genomics
Phylogenomics
Phylogeny
Added:
Comparative Genomics
Phylogenomics
Phylogeny
Removed:
'dataProcesses' has been modified:
Before:
Sequence search
After:
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
Removed:
Sequence search
'onto_domains' has been modified:
Before:
After:
Protein domain
conserved_region
genome
homologous
orthologous
Added:
Protein domain
conserved_region
genome
homologous
orthologous
Removed:
'tools' has been modified:
Before:
After:
BLAST||https://chlamdb.ch/blast/
Plot Genomic Region||https://chlamdb.ch/plot_region/
Circos Plots||https://chlamdb.ch/circos/
Added:
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
Related Standards
Reporting Guidelines
No guidelines defined
Terminology Artifacts
No semantic standards defined
Models and Formats
No syntax standards defined
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
Implementing Policies
This record is not implemented by any policy.
We need your help!
Do you have 5-10 minutes to help FAIRsharing prioritize future enhancements?
Then please fill out this short questionnaire to
prioritise the improvements that are of greatest importance to you.
Your views will help us choose which enhancements to provide first. Thank you very much!
