Exalign

Exalign analyzes exon–intron structures in gene annotations to compare gene structural organization alongside sequence comparisons and support evolutionary inference.

Key Features:

• Exon–Intron Structure Retrieval and Comparison: Retrieves and compares exon–intron structures from gene annotations to characterize structural differences among genes.
• Integration with Sequence Comparisons: Combines exon–intron structural analysis with traditional genomic, transcript, and protein sequence comparisons.
• Structure-based Phylogenetic Inference: Uses exon–intron structural data to aid phylogenetic reconstruction and clarify relationships among homologous gene families.
• Intron Gain and Loss Detection: Detects intron loss events in human and rodent genomes and identifies novel intron gain events in human and mouse genes.
• Structure Search and Comparison Algorithm: Implements algorithmic comparison and search of exon–intron structures within annotations to uncover evolutionary patterns.

Scientific Applications:

• Phylogenetic Analyses: Improves phylogenetic resolution by incorporating exon–intron structure as additional characters.
• Evolutionary History Reconstruction: Supports reconstruction of evolutionary histories of homologous gene families through structural comparisons.
• Intron Gain/Loss Studies: Facilitates detection and characterization of intron gain and loss patterns across human, mouse, and rodent lineages.

Methodology:

A dedicated algorithm extracts exon–intron structures from gene annotations and performs comparison and search of these structures to detect intron gain and loss and inform phylogenetic inference.