GenVision

GenVision visualizes genomic features and multi-attribute relationships to analyze large-scale bacterial genomes and compare predictions such as horizontal gene transfer.

Key Features:

• Intuitive visualization: Visualizes correlations among properties across core datasets to aid interpretation of large genomic datasets.
• Simultaneous multi-attribute display: Java-based implementation displays multiple attributes of genes and intragenic regions within a single bacterial genome using distinct colors and shapes, representing each gene as a small box at its physical genome position.
• Dynamic scaling and zooming: Dynamically allocates box sizes based on gene count and provides zooming for inspection of specific genomic regions.
• Database integration: Interfaces with an MS-Access relational database to display any feature represented by discrete values.
• Data import flexibility: Imports new data from MS-Excel spreadsheets into the MS-Access database.
• Publication-quality outputs: Integrates with Lasergene to generate high-quality graphics and genome maps suitable for publication.
• Combinatorial correlation expansion: Addition of features exponentially increases the number of possible correlations that can be visualized.

Scientific Applications:

• Horizontal gene transfer comparison: Visual comparison of horizontal gene transfer predictions in Synechocystis PCC-6803 to assess agreement between different prediction methods.
• Gene distribution analysis: Visualization of gene distribution across categories (e.g., genes predicted by both methods or only one) to inform genomic organization and evolutionary studies.
• Bacterial genomics and beyond: Application in bacterial genomics and extendable to other contexts such as patient studies for complex dataset visualization.

Methodology:

Represents genes as boxes positioned by physical genome coordinates, encodes multiple attributes using colors and shapes, dynamically adjusts box sizes based on gene count, provides zooming, interfaces with MS-Access and imports from MS-Excel, and enables visual comparison of prediction outputs such as horizontal gene transfer predictions.