fagin

fagin applies synteny-based phylostratigraphy to classify genes and estimate gene age by integrating syntenic context with homology relationships.

Key Features:

• Synteny-Based Analysis: Identifies homologs within syntenic regions across species and integrates synteny with protein similarity-based phylostratigraphy to refine gene age estimates and de novo/orphan identification.
• Gene Classification: Classifies genes into AAic (Ancestral Coding Syntenic Homolog), NTic (Non-Coding Syntenic Homolog), and Unknown categories based on detected syntenic homology relationships.
• Automated and Customizable Pipeline: Provides an automated computational pipeline configurable for contextual analysis to distinguish rapidly diverged genes from genes originating de novo.
• Empirical Testing Across Taxa: Applied to Arabidopsis thaliana with four Brassicaceae target species and Saccharomyces cerevisiae with six Saccharomyces target species to demonstrate cross-taxon applicability.
• Identification of Genomic Perturbations: Compares synteny-based phylostrata to standard phylostrata to identify orphans and lineage-specific genes and to distinguish absence of syntenic homologs due to local indels, scrambled synteny, or other genomic perturbations.
• Implementation: Implemented within the R programming framework.

Scientific Applications:

• Gene origin inference: Refines phylostratigraphic age estimates to separate de novo-origin genes from rapidly diverged homologs.
• Evolutionary genomics: Supports studies of species-specific genetic innovation and the evolutionary history of genes across lineages.
• Genome stability analysis: Identifies regions of high genomic perturbation to inform investigations of genome structural variation and its evolutionary consequences.

Methodology:

Uses synteny-based identification of homologs and comparison of synteny-based phylostrata to standard protein similarity-based phylostrata, classifies genes into AAic, NTic, or Unknown, and is implemented in R.