Titre
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum.
Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
Auteur(s)
Pillonel, T.
Auteure/Auteur
Tagini, F.
Auteure/Auteur
Bertelli, C.
Auteure/Auteur
Greub, G.
Auteure/Auteur
Liens vers les personnes
Liens vers les unités
ISSN
1362-4962
Statut éditorial
Publié
Date de publication
2020-01-08
Volume
48
Numéro
D1
Première page
D526
Dernière page/numéro d’article
D534
Peer-reviewed
Oui
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Résumé
ChlamDB is a comparative genomics database containing 277 genomes 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. Gene annotations from multiple databases including UniProt (curated and automated protein annotations), KEGG (annotation of pathways), COG (orthology), TCDB (transporters), STRING (protein-protein interactions) and InterPro (domains and signatures) can be accessed in a comprehensive overview page. 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, integrates multiple tools for comparative genomic analyses and is freely available at https://chlamdb.ch/. Database URL: https://chlamdb.ch/.
PID Serval
serval:BIB_60D235C6962F
PMID
Open Access
Oui
Date de création
2020-06-18T08:00:30.070Z
Date de création dans IRIS
2025-05-20T13:47:57Z
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Nom
31665454_BIB_60D235C6962F.pdf
Version du manuscrit
published
Licence
https://creativecommons.org/licenses/by/4.0
Taille
4.98 MB
Format
Adobe PDF
PID Serval
serval:BIB_60D235C6962F.P001
URN
urn:nbn:ch:serval-BIB_60D235C6962F1
Somme de contrôle
(MD5):0e69e54d1b7b2e8a7da9829edf9921e1