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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.

Homepage https://chlamdb.ch/

Countries that developed this resource Switzerland

Created in 2015

Taxonomic range

Knowledge Domains

Subjects

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: Dec 08 2021 12:52 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;

This record is maintained by Tpillonel

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

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:

In Collections

RDA Covid-19 WG Resources

Support

General

help	Report an Issue
online documentation	Documentation
online documentation	About ChlamDB

Additional Information

Contact

Trestan Pillonel ORCID

Tools

BLAST	https://chlamdb.ch/blast/
Plot Genomic Region	https://chlamdb.ch/plot_region/
Circos Plots	https://chlamdb.ch/circos/

Access / Retrieve Data

Conditions of Use

Data Access

Extract Genomic Region	https://chlamdb.ch/extract_region/
Extract Orthogroups	https://chlamdb.ch/extract_orthogroup/
Extract COGs	https://chlamdb.ch/extract_cog/
Extract Pfam Domains	https://chlamdb.ch/extract_pfam/
Extract InterPro Entries	https://chlamdb.ch/extract_interpro/
Extract KEGG Orthologs	https://chlamdb.ch/extract_ko/
TCDB Annotation Search	https://chlamdb.ch/transporters/
View KEGG Maps	https://chlamdb.ch/priam_kegg/
View KEGG Modules	https://chlamdb.ch/kegg_module/

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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This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by Tpillonel

Maintains

Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Switzerland (University) Lead

Chlamydiae Database

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