Asymmetry

Asymmetry analyzes amino acid substitution patterns in protein sequences to quantify directional substitutions between mesophilic and thermophilic organisms and reveal selection biases related to temperature adaptation.

Key Features:

• AmbiguityRemover: Processes protein sequence alignments to eliminate ambiguously aligned sites and produce high-confidence alignment data.
• AsymmetryCounter: Quantifies directional amino acid substitutions between pairs of protein sequences by identifying and counting non-symmetric amino acid replacements.
• AsymmetryScaler: Aggregates and scales substitution counts from AsymmetryCounter to present substitutional asymmetry on a unified scale for comparative interpretation.

Scientific Applications:

• Evolutionary and temperature-adaptation studies: Analyzes how amino acid substitution patterns differ between mesophiles and thermophiles to infer evolutionary pressures and selection biases.
• Comparative genomics (Methanococcus vs Bacillus): Compares protein sequences from the archaeal genus Methanococcus and the bacterial genus Bacillus to detect dramatically asymmetrical substitution patterns between these genera.
• Correlation with DNA G + C content: Investigates how differences in DNA G + C content may relate to observed asymmetrical amino acid substitution patterns.

Methodology:

Removes ambiguously aligned sites from protein sequence alignments; quantifies directional amino acid substitutions between sequence pairs by counting non-symmetric replacements; synthesizes substitution counts into a unified asymmetry scale.