SWAKK

SWAKK identifies amino acid sites and regions under positive selection by calculating Ka/Ks (the ratio of non-synonymous to synonymous substitution rates) between pairs of protein-coding DNA sequences using sliding-window analyses on protein structures or primary sequences.

Key Features:

• Ka/Ks calculation: Computes Ka/Ks as the ratio of non-synonymous to synonymous substitution rates between pairs of protein-coding DNA sequences using sliding-window analysis.
• 3D spherical sliding window: Applies a sliding 3D window conceptualized as a sphere across a reference protein structure to assess regional selection pressures.
• Sequence-based sliding window: Performs sliding-window analyses on the primary amino-acid sequence when a reference structure is unavailable.
• Structural mapping of selection: Maps Ka/Ks results onto 3D protein structures to highlight regions with elevated Ka/Ks ratios indicative of adaptive evolution.
• Detection granularity: Identifies individual amino acid sites and contiguous regions exhibiting signals of positive selection.

Scientific Applications:

• Detection of positive selection: Identification of amino acid sites and regions under positive selection between sequence pairs.
• Molecular evolution studies: Analysis of region-specific selective pressures to infer evolutionary dynamics of proteins.
• Functional genomics: Correlation of adaptive changes with structural regions to investigate potential impacts on protein function and stability.
• Comparative sequence analysis: Pairwise comparison of protein-coding DNA sequences to detect adaptive divergence.

Methodology:

Sliding-window analysis of Ka/Ks between pairs of protein-coding DNA sequences, using either a 3D spherical window across a reference protein structure or a sequence-based sliding window, with results mapped onto 3D structures when available.