Numerical encoding of DNA sequences by Chaos Game Representation

Numerical encoding of DNA sequences by Chaos Game Representation encodes DNA sequences using the Chaos Game Representation to transform nucleotide sequences into numerical (complex) series for digital signal processing and comparative evolutionary analysis.

Key Features:

• One-to-One Mapping: The Chaos Game Representation produces a one-to-one correspondence between the original DNA sequence and its numerical representation, preserving sequence information.
• Complex Number Representation: Two-dimensional CGR coordinates are interpreted as complex numbers to represent DNA sequences numerically.
• Digital Signal Processing Integration: Numerical representations are analyzed with digital signal processing methods, including the discrete Fourier transform.
• Comparative Performance with Clustal Omega: Computational experiments reported results comparable to the multiple sequence alignment method Clustal Omega while being significantly faster.

Scientific Applications:

• Phylogenetic Analysis: Construction of phylogenetic trees and assessment of evolutionary relationships among DNA sequences.
• Sequence Comparison and Alignment: Numerical transformation of sequences to enable efficient comparison and alignment for identifying conserved regions and mutations.
• Evolutionary Studies: Comparative analyses to explore evolutionary dynamics and lineage divergence.

Methodology:

Encode DNA sequences by mapping each nucleotide to 2D coordinates via the Chaos Game Representation, interpret the coordinates as complex numbers, and apply digital signal processing techniques such as the discrete Fourier transform to analyze the numerical series.