chaos

chaos generates chaos game representation (CGR) plots to visualize nucleotide (DNA and RNA) sequence composition and patterning for genomic analysis.

Key Features:

• Visualization Technique: Produces fractal-based CGR images by mapping nucleotide symbols onto coordinates in a two-dimensional square grid to reveal sequence patterns.
• Integration with EMBOSS: Implemented within the EMBOSS suite and interoperates with the suite's applications and third-party software.
• Extensibility and Customization: Implemented using EMBOSS C libraries and supports Application Configuration Description (ACD) files for modification and development.

Scientific Applications:

• Genomic Analysis: Identifies repetitive elements, palindromic structures, and sequence motifs by visualizing nucleotide composition and local patterns.
• Comparative Genomics: Highlights similarities and differences in sequence patterning between genomes and across species using CGR comparisons.
• Structural Biology: Provides nucleotide pattern information that can inform analyses of DNA three-dimensional structure and protein-DNA interaction hypotheses.

Methodology:

The method maps each nucleotide to a specific point on a square grid, starts from an initial random position within the grid, and iteratively plots points by moving halfway toward the nucleotide's target point for each successive base, producing a fractal pattern that reflects the underlying sequence composition.