clustermap.js

clustermap.js generates comparative visualizations of gene clusters and orders clusters by sequence similarity to support homology assessment and evolutionary analysis.

Key Features:

• Automatic data processing: Operates with clinker to extract protein translations from GenBank files and perform global alignments between sequences within each cluster.
• Optimal display order determination: Calculates similarity metrics and determines an optimal ordering of gene clusters based on sequence similarity.
• Visualization generation: Generates visualizations using D3.js and exports scalable vector graphics (SVG) for downstream analysis and publication.
• Pipeline integration: Interoperates with clinker (Python) to convert sequence files into comparative cluster figures.

Scientific Applications:

• Comparative genomics: Visualizes and compares gene cluster organization and homology across different organisms or experimental conditions.
• Evolutionary analysis: Assists analysis of gene cluster evolution and conservation of biological pathways.
• Functional inference: Facilitates exploration of homologies and functional relationships among genes within and between clusters.

Methodology:

Automated extraction of protein translations from GenBank files; execution of global sequence alignments within gene clusters; calculation of similarity metrics to determine optimal cluster ordering; generation of visualizations using D3.js and export to SVG.