GEnView

GEnView performs comparative analysis of gene loci across bacterial genomes and plasmids to investigate conservation, acquired mobility, and horizontal gene transfer.

Key Features:

• Automated comparative analysis: Performs automated locus-level comparisons across bacterial genomes and plasmids with taxon-selective access to over 800,000 genomes and plasmids in the NCBI Assembly and RefSeq databases.
• Local genome processing: Processes local (non‑NCBI) genome and plasmid assemblies to include proprietary or unpublished datasets in analyses.
• Visualization of genetic environments: Produces visual representations of genetic neighborhoods surrounding target loci to contextualize gene content and synteny.
• Extensive metadata generation: Generates comprehensive metadata files accompanying analyses for downstream research and validation.

Scientific Applications:

• Bacterial comparative genomics: Enables comparison of gene loci across strains and species to assess conservation and structural variation.
• Mobilome and horizontal gene transfer studies: Facilitates investigation of acquired mobility and horizontal gene transfer events associated with specific loci.
• Evolutionary analyses of loci: Supports studies of evolutionary processes affecting gene neighborhoods across taxa.

Methodology:

Implemented in Python 3, GEnView automates retrieval of genomic data from NCBI Assembly and RefSeq and from local sources, performs locus-level comparisons, generates metadata, and provides a visualization component for genetic contexts.