GLASS

GLASS aligns pairs of homologous sequences to detect conserved exon and intron structures and support gene recognition across long or divergent orthologous and paralogous gene pairs.

Key Features:

• Iterative global alignment system: Employs an iterative global alignment approach to align long and divergent sequences containing blocks of moderate to strong homology.
• Cross-species comparative analysis: Compares orthologous genomic loci, exemplified by human and mouse, to assess conservation across species.
• Exon–intron assessment: Evaluates exon and intron numbers, sizes, and sequences within aligned regions.
• Gene recognition via conserved exonic features: Identifies genes based on conserved exonic features at aligned positions between species.
• Integration with ROSETTA: Operates in tandem with the ROSETTA program, which recognizes coding exons within aligned orthologous pairs.
• Empirical validation: Demonstrated performance in evaluations of 117 orthologous gene pairs, with ROSETTA showing high accuracy in identifying exact coding exons using GLASS alignments.

Scientific Applications:

• Cross-species genomic comparison: Aligns orthologous loci to study conservation of gene structure between species such as human and mouse.
• Comparative genomics and evolutionary biology: Illuminates conservation of exon–intron architecture and genome evolution across orthologous and paralogous genes.
• Gene annotation and recognition: Facilitates identification of coding exons and gene structures through conserved exonic alignments.

Methodology:

Performs comparative analysis of orthologous genomic loci (e.g., human and mouse) assessing exon and intron numbers, sizes, and sequences; applies an iterative global alignment system to align these regions accurately; identifies genes based on conserved exonic features at aligned positions and interfaces with ROSETTA to pinpoint coding exons.