Clinker is a command-line tool designed to generate figure comparisons of gene clusters. It takes GenBank files as input and facilitates the visualization of gene clusters within a biological context. Clinker performs pairwise alignments of sequences within clusters and employs the clustermap.js library to produce interactive visualizations as SVG files. It primarily relies on the BioPython aligner for sequence alignment.
Clinker simplifies the creation of gene cluster comparison figures, streamlining a complex workflow. It leverages clustermap.js for interactive visualization, allowing users to explore and analyze cluster relationships. The tool supports both whole genome alignment and functional grouping based on gene functions, offering flexibility in analysis scope and highlighting connections between different clusters. It provides interactive plots and options for customization such as plot saving and color mapping.
- Sequence Alignment: Performs pairwise alignments between all sequences within gene clusters using BioPython's aligner.
- Interactive Visualization: Generates interactive, to-scale comparison figures using the clustermap.js library.
- Functional Grouping: Supports defining gene groups based on function using a CSV file, allowing for meaningful clustering of homologous genes.
- Customizable Plots: Offers various customization options including plot saving, color mapping, and control over display headers.
- Flexible Input: Accepts GenBank files and GFF3 files, offering adaptability to different data formats.
- Parallel Processing: Supports parallel processing of alignments for improved performance.
- Command-Line Interface: Provides a user-friendly command-line interface for easy execution and parameter configuration.
Clinker has been actively developed and maintained, with recent updates and bug fixes. The project has a history of releases and a supportive community, indicated by the number of stars and forks on GitHub. Documentation is available, though it could be further enhanced. The base functionality is established, but performance may be a concern with very large datasets.
Clinker benefits researchers by offering a straightforward way to visualize gene cluster relationships, aiding in the understanding of genomic organization and potential functional interactions. It's valuable for anyone studying biosynthetic gene clusters or other genomic regions composed of closely related genes. It provides a user-friendly alternative to manual alignment and visualization methods, streamlining data analysis workflows.