LAGAN

LAGAN performs rapid, accurate global alignment of homologous genomic sequences across species to identify conserved protein-coding exons and other conserved genomic elements in long genomic regions.

Key Features:

• Rapid Alignment: Performs global alignments of genomic regions up to several megabases within minutes.
• High Accuracy: Accurately aligns protein-coding exons between distantly related species such as human and chicken or human and fugu.
• Multiple Sequence Alignment: The Multi-LAGAN extension facilitates multiple global alignment and demonstrated alignment of over 12 Mb of high-quality sequence from 12 vertebrate species derived from a region orthologous to ~1.5 Mb on human chromosome 7q31.3.
• Efficiency: Multi-LAGAN can produce comprehensive multiple alignments for all sequences within 75 minutes on a personal computer.

Scientific Applications:

• Comparative Genomics: Enables cross-species genome comparisons to identify conserved genetic features and evolutionary relationships.
• Functional Genomics: Supports analysis of gene structure and regulatory conservation by accurately aligning protein-coding exons across organisms.
• Evolutionary Studies: Facilitates analyses of evolutionary conservation and phylogenetic relationships through alignment of distant homologs.

Methodology:

LAGAN is built upon the CHAOS local alignment tool and employs rapid global alignment techniques that emphasize efficiency and scalability.