EGIO

EGIO detects orthologous exons and orthologous isoforms between two species by constructing exon groups from unique exonic regions and aligning them with a dynamic programming strategy to comprehensively cover coding exons within orthologous genes.

Key Features:

• Exon group ideogram: Constructs exon groups based on unique exonic regions to represent exon correspondences between species.
• Dynamic programming alignment: Aligns exon groups using a dynamic programming strategy to identify orthologous relationships.
• Comprehensive coding exon coverage: Ensures coverage of all coding exons within orthologous genes during detection.
• Orthologous isoform detection: Detects orthologous isoforms with conserved sequence and exon structures and reports higher sensitivity compared to ExTraMapper in the reported analyses.

Scientific Applications:

• Comparative genomics: Identifies orthologous exons and isoforms between two species to inform cross-species transcriptome comparisons.
• Alternative splicing analysis: Assesses transcriptomic diversity by detecting conserved and species-unique isoforms based on exon structure and sequence conservation.
• Evolutionary transcriptomics: Applied to human and chimpanzee frontal cortex protein-coding isoforms to identify genes expressing human-unique isoforms (reported 6,912 genes).

Methodology:

Constructs exon groups from unique exonic regions and aligns those exon groups using a dynamic programming strategy to achieve comprehensive coverage of coding exons within orthologous genes.