CoreTracker

CoreTracker predicts sense-to-sense codon reassignments in mitochondrial and other genomes within a phylogenetic framework to detect genetic code variations and trace their evolution.

Key Features:

• Phylogenetic framework: Evaluates sets of related genomes simultaneously within a phylogenetic context, enabling tracing of codon reassignment evolution and contrasting with single-genome tools such as FACIL, GenDecoder, and Bagheera.
• Statistical evaluation and machine learning: Combines statistical evaluations with a random forest classifier to predict potential sense-to-sense codon reassignments and reduce false positives.
• Phylogeny-aware validation: Implements a phylogeny-aware validation step that assesses the impact of predicted genetic code changes on protein alignments to filter unlikely reassignments.
• Application to diverse genomes: Applied to metazoan and yeast genomes to detect genetic code variations across different evolutionary contexts, including mitochondrial genomes.

Scientific Applications:

• Evolutionary biology: Identifying and tracing codon reassignments across related genomes to study the evolution of the genetic code.
• Mitochondrial genomics: Characterizing mitochondrial genetic code variations and their consequences for mitochondrial protein translation and annotation.
• Comparative genomics and annotation: Improving genome annotation and downstream analyses in metazoan and yeast datasets by accurate detection of codon reassignments.

Methodology:

Performs multi-genome phylogenetic evaluation, applies statistical assessments combined with a random forest classifier to predict sense-to-sense reassignments, and carries out a phylogeny-aware validation step that evaluates predicted genetic code changes on protein alignments.