"Using Multiple Alignments and Phylogenetic Trees to Detect RNA
Secondary Structure"
Brad Gulko and David Haussler
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.