KaKs_Calculator

KaKs_Calculator 3.0 calculates selective pressure on coding and non-coding genomic sequences by estimating substitution rate ratios analogous to nonsynonymous/synonymous rates for coding regions and by comparing non-coding nucleotide substitution rates to synonymous substitution rates in adjacent coding regions.

Key Features:

• Selective Pressure Calculation: Quantifies selective pressure for coding sequences using a ratio analogous to nonsynonymous/synonymous substitution rates and for non-coding sequences using the ratio of non-coding nucleotide substitution rates relative to synonymous rates in adjacent coding regions.
• Empirical Validation: Validated with empirical data for detecting both the strength and the mode of selection acting on molecular sequences.
• Genome-wide Analysis: Performs genome-wide scans of substitution rate ratios to identify potentially functional elements across coding and non-coding regions.

Scientific Applications:

• Investigating selective pressures: Quantifies selective constraints across entire genomes including both coding and non-coding regions.
• Identifying functional non-coding elements: Detects constrained non-coding regions by comparing non-coding substitution rates to synonymous rates in adjacent coding sequences.
• Comparative evolutionary studies: Enables comparison of selective forces shaping genomes between species or genomic regions.

Methodology:

Calculates substitution rate ratios (analogous to dN/dS for coding regions) and computes ratios of non-coding nucleotide substitution rates relative to synonymous substitution rates in adjacent coding regions to infer selective pressures.