zDB

zDB performs comparative genomics analyses by automating orthology prediction, functional annotation, and phylogenetic inference to support evolutionary and comparative studies.

Key Features:

• Integrated Analysis Pipeline: A Nextflow-based pipeline processes annotated GenBank files to identify orthologs and infer phylogenies for each orthogroup and to construct species phylogenies from shared single-copy orthologs.
• Annotation Sources: Functional annotations are integrated from Pfam protein domains, Cluster of Orthologous Groups (COGs), KEGG pathways, Swissprot homologs, and RefSeq.
• Orthology and Phylogenetic Inference: Orthology prediction and phylogenetic reconstruction are performed per orthogroup and aggregated to generate species-level phylogenies using single-copy orthologs.
• Sequence Similarity Searches: BLAST queries are supported for sequence-level comparisons and homology searches.
• Comparative Metabolic and Conservation Analysis: Comparative analyses quantify metabolic capacity at module and pathway levels and assess gene or annotation conservation across selected genome subsets.
• Visualization Outputs: Results can be exported or rendered as lists, Venn diagrams, and heatmaps for comparative and presence/absence analyses.

Scientific Applications:

• Comparative Genomics: Comparative analysis of gene content, orthogroups, and annotations across datasets ranging from a few genomes to hundreds of genomes.
• Evolutionary Inference: Reconstruction of orthogroup phylogenies and species phylogenies to study evolutionary relationships.
• Functional and Metabolic Profiling: Assessment of pathway and module presence to compare metabolic capacities and functional repertoire among organisms.

Methodology:

A Nextflow-based pipeline ingests annotated GenBank files, performs ortholog identification and orthogroup phylogenetic inference, constructs species phylogenies from shared single-copy orthologs, integrates annotations from Pfam, COGs, KEGG, Swissprot, and RefSeq, supports BLAST queries, and generates comparative outputs including lists, Venn diagrams, and heatmaps.