zDB: bacterial comparative genomics made easy

Genome comparison and analysis rely on many independent tools, leaving to scientists the burden to integrate and visualize their results for interpretation. To alleviate this burden, we have built zDB, a comparative genomics tool that includes both an analysis pipeline and a visualization platform....

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Veröffentlicht in:mSystems Jg. 9; H. 7; S. e0047324
Hauptverfasser: Marquis, Bastian, Pillonel, Trestan, Carrara, Alessia, Bertelli, Claire
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States American Society for Microbiology 23.07.2024
Schlagworte:
Annotations
comparative genomics
Datasets
Genes
genome visualization
Genomes
Genomic analysis
Genomics
Interfaces
Metabolic pathways
Methods and Protocols
Microbial Genetics
microbial genomics
Orthology
Phylogenetics
Phylogeny
Predictions
Proteins
Visualization
comparative genomics
microbial genomics
genome visualization
ISSN:2379-5077, 2379-5077
Online-Zugang:Volltext
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Beschreibung
Zusammenfassung:Genome comparison and analysis rely on many independent tools, leaving to scientists the burden to integrate and visualize their results for interpretation. To alleviate this burden, we have built zDB, a comparative genomics tool that includes both an analysis pipeline and a visualization platform. The analysis pipeline automates gene annotation, orthology prediction, and phylogenetic inference, while the visualization platform allows scientists to easily explore the results in a web browser. Among other features, the interface allows users to visually compare whole genomes and targeted regions, assess the conservation of genes or metabolic pathways, perform Blast searches, or look for specific annotations. Altogether, this tool will be useful for a broad range of applications in comparative studies between two and hundred genomes. Furthermore, it is designed to allow sharing of data sets easily at a local or international scale, thereby supporting exploratory analyses for non-bioinformaticians on the genome of their favorite organisms.
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The authors declare no conflict of interest.
ISSN:2379-5077
2379-5077
DOI:10.1128/msystems.00473-24