Selectome

Selectome identifies and catalogs instances of positive selection in gene sequences across species by applying branch-site likelihood tests to estimate nonsynonymous (dN) to synonymous (dS) substitution ratios at sites and along evolutionary branches.

Key Features:

• Branch-Site Likelihood Test: Implements a branch-site likelihood test model to detect site- and branch-specific positive selection.
• dN/dS Estimation: Estimates nonsynonymous (dN) to synonymous (dS) substitution ratios to quantify selective pressures.
• Quality Control on Alignments: Applies quality-control procedures to multiple sequence alignments to minimize false positives.
• Computational Efficiency: Uses an optimized implementation of the branch-site test to enable analysis of larger datasets.
• Gene Tree Coverage: Analyzes gene trees from Ensembl for Primates and Glires and a substantial collection of vertebrate gene trees, with evidence of positive selection reported in 6810 gene trees.

Scientific Applications:

• Adaptive Evolution Detection: Detects and catalogs positively selected sites and lineages to study adaptive changes at the molecular level.
• Comparative Genomics: Supports comparative analyses among Primates, Glires (rodents and lagomorphs), and other vertebrates using Ensembl gene trees.
• Molecular Evolution and Genetics: Provides site- and branch-specific estimates of selective pressure for molecular-evolution and genetic studies.

Methodology:

Applies the branch-site likelihood test to estimate dN/dS ratios, employs quality-control procedures on multiple sequence alignments, uses an optimized implementation for computational efficiency, and performs analyses on Ensembl gene trees for Primates, Glires, and vertebrates.