zDB

A comparative genomics database

The database contains:

Genomes

Display the summary table of the genomes contained in the database and navigate to the list of proteins for each of them.
Fasta files and .gbk files are available for downloading.


Phylogeny

Visualize and download the phylogenetic tree built on concatenated single copy orthologs. The phylogeny is annotated with genomics info, such as genome size, GC content, coding density, completness, and contamination expressed as percentages.

Homology search

Blast an input sequence against the genomes of the database. You can select among blastn, blastp, or the six-frame translation-based approaches, blastx and tblastn.


Orthology

Get a list of Orthogroups shared by selected genomes and absent in others and display the result in a Venn diagram for an easier understanding or visualize their presence or absence in heatmaps. Identify orthogroups presenting more than one homolog in genomes of interest and draw barcharts to visualize the distribution of selected categories among the genomes.


Annotations

Get a list of COG entries, Pfam domains, Kegg Orthologs, AMR genes, Virulence factors shared by selected genomes and absent in others and display the result in a Venn diagram for an easier understanding or visualize their presence or absence in heatmaps. Identify orthogroups presenting more than one homolog in genomes of interest and draw barcharts to visualize the distribution of selected categories among the genomes.


Genome alignments

Generate a clickable version of circos plot indicating the presence/absence of homologous proteins in one or multiple genomes, the GC content and navigate to the description of the locus tags of interest.


Align target genomic regions of two or more genomes and plot them.

Metabolism

Discover which metabolic pathways are present in the genomes. KEGG categories can be investigated checking which KEGG entries are present in each KEGG module. Entries can be visualized in lists or used to generate an annotated phylogeny. In addition, you can visualize in the KEGG maps which genes of a specific pathway are carried by a genome of interest.



Custom plots

Produce phylogenetic trees and tables including annotations of your choice.

Genome Groups

Overview of defined groups of genomes.






Status of your database

Your database has been generated including the following features:

  • Orthologous proteins identified with OrthoFinder
  • Detailed annotation of proteins based on:
    - COG (clusters of orthologous groups, reference DB version 3.21)
    - Pfam (protein families, reference DB version 37.0)
    - KEGG (Kegg orthologs, reference DB version 2022-03-01)
    - SwissProt (manually annotated proteins, reference DB version 2024_05)
    - AMRFinderPlus (4.0.3) (manually annotated Antiobiotic resistance genes, reference DB version 2024-10-22.1)
    - VFDB (curated database of virulence factors of bacterial pathogens, reference database 2024-11-01)
  • Precomputed phylogenetic reconstructions of orthologous groups
  • Kegg maps visualization
  • Genomes alignments can be visualized with Circos and selected regions can be plotted and compared