clinker

clinker performs comparative analysis and visualization of homologous genes across multiple gene clusters by extracting protein translations from GenBank and identifying homology via global alignments.

Key Features:

• Automatic processing: Extracts protein translations directly from GenBank files for downstream comparison.
• Global alignment and analysis: Performs global alignments between sequences within clusters to identify homologous relationships.
• Optimal display order determination: Computes cluster similarity to determine an informative display order for comparative visualization.
• Interactive visualization: Generates interactive homology visualizations using clustermap.js built on d3.js to represent relationships among multiple gene clusters.
• Exportable vector graphics: Supports customization of visualizations and exports figures as SVG.

Scientific Applications:

• Functional genomics: Compares gene cluster content and homology to support inference of gene function within biological pathways.
• Evolutionary biology: Reveals patterns of gene conservation and divergence to inform the evolutionary history of gene clusters across organisms.

Methodology:

Input GenBank files; extract protein translations; perform global sequence alignments to identify homologues; compute cluster similarity to determine display order; generate interactive visualizations with clustermap.js (based on d3.js) and export as SVG.