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Using multiple alignments and phylogenetic trees to detect RNA secondary structure
1Department of Computer Engineering, Lepton Incorporated, University of California at Santa Cruz, USA. bgulko@LeptonCorp.com
Abstract:
We describe a statistical method to determine if a pair of columns in a multiple alignment of a homologous family of RNA sequences shows evidence of being base paired. The method makes explicit use of a given phylogenetic tree for the sequences in the alignment. It is tested on a multiple alignment of 16S rRNA sequences with good results.