ExOrthist

ExOrthist infers exon orthology groups and exon homology relationships genome-wide across evolutionary distances to analyze exon sequence and exon-intron structural conservation and the evolution of alternative splicing.

Key Features:

• Exon Homology Inference: Detects exon homologous relationships and groups exons into orthogroups across genomes.
• Multi-Species Analysis: Derives genome-wide multi-species exon homologies applicable across diverse evolutionary distances.
• Contextual Evaluation: Evaluates exon sequence conservation together with surrounding exon-intron context, including intron positions and phases.
• Evolutionary Insights: Provides visualization of exon-intron structural evolution and conservation of alternative splicing patterns.
• Nextflow-based Reproducibility: Implemented as a Nextflow-based pipeline to enable reproducible and scalable computational workflows.

Scientific Applications:

• Evolutionary exon homology analysis: Investigates exon conservation to inform gene function and regulatory evolution.
• Whole genome duplication studies: Applied to study exon homology changes in whole genome duplications, including analyses in frogs.
• Splicing network evolution: Analyzes conservation and convergence of Nova-regulated splicing networks and alternative splicing patterns.

Methodology:

Implemented as a Nextflow-based pipeline that sequentially evaluates (1) conservation of up/downstream intron positions and phases, (2) conservation of exon sequence, and (3) conservation of up/downstream exon sequences.