Gene Graphics

Gene Graphics visualizes genomic neighborhoods and generates publication-quality graphics for gene clusters to support comparative genomics.

Key Features:

• Input Formats: Supports National Center for Biotechnology Information (NCBI) gene and protein identifiers, GenBank files, and data extracted from the SEED database.
• Automatic Data Fetching: Automatically retrieves neighboring gene information based on provided identifiers or GenBank files.
• Customization Options: Allows specification of gene and genome representation parameters including names, colors, and sizes.
• Export Formats: Exports figures as Portable Network Graphics (PNG), Scalable Vector Graphics (SVG), Tagged Image File Format (TIFF), and Encapsulated PostScript (EPS).
• Publication-quality Output: Produces graphics tailored for gene clusters suitable for inclusion in scientific publications.

Scientific Applications:

• Comparative genomics: Visualization of gene neighborhoods across genomes to compare gene order and context between species.
• Evolutionary analysis: Examination of conserved or rearranged gene clusters to infer evolutionary relationships.
• Functional conservation inference: Assessment of co-localized genes and clusters to support hypotheses of shared function or operon structure.
• Genomic architecture visualization: Representation of gene cluster organization to analyze locus structure and neighboring gene content.

Methodology:

Automated retrieval of neighboring gene information from NCBI/GenBank/SEED using provided gene or protein identifiers or GenBank files, followed by rendering of gene-cluster visualizations exportable as PNG, SVG, TIFF, and EPS.