ARNA: Interactive Comparison and Alignment of RNA Secondary Structure

ARNA is an interactive visualization system that supports comparison and alignment of RNA secondary structure. We present a new approach to RNA alignment that exploits the complex structure of the Smith-Waterman local distance matrix, allowing people to explore the space of possible partial alignments to discover a good global solution. The modular software architecture separates the user interface from computation, allowing the possibility of incorporating different alignment algorithms into the same framework.