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Phylogenetic reconstructions based on RNA secondary structure

Date: 
Monday 3rd September 2007 - 16:10 to 16:30
Venue: 
INI Seminar Room 1
Abstract: 

It is known that RNA secondary structure motifs are usually conserved, and have a vital influence on the activity of the RNA molecules. We present a novel approach for phylogenetic reconstruction, based on comparing secondary structures of homologous RNA molecules from different species. By manipulating the RSmatch algorithm for measuring RNA secondary structure similarity, we computed pairwise distances between secondary structures. Consequently, we applied the neighbor joining algorithm on the distance matrix, to produce phylogenetic trees. Initial analysis of the results exhibits a good agreement with the accepted taxonomy. Comparison with the trees based RNA sequences alone have also produced favorable results.

This is joint work with Moran Cabili, Assaf Meirovich, and Metsada Pasmanik-Chor

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University of Cambridge Research Councils UK
    Clay Mathematics Institute London Mathematical Society NM Rothschild and Sons