UCSC-CRL-96-06: USING PHYLOGENETIC MARKOV TREES TO DETECT CONSERVED STRUCTURE IN RNA MULTIPLE ALIGNMENTS

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Published On 03/01/1996 09:00 AM

Department Biomolecular Engineering

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.

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UCSC-CRL-96-06