Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.

ABSTRACT: RNA binding proteins recognize RNA targets in a sequence specific manner. Apart from the sequence, the secondary structure context of the binding site also affects the binding affinity. Binding sites are often located in single-stranded RNA regions and it was shown that the sequestration of a binding motif in a double-strand abolishes protein binding. Thus, it is desirable to include knowledge about RNA secondary structures when searching for the binding motif of a protein. We present the approach MEMERIS for searching sequence motifs in a set of RNA sequences and simultaneously integrating information about secondary structures. To abstract from specific structural elements, we precompute position-specific values measuring the single-strandedness of all substrings of an RNA sequence. Thes

SUBMITTER: Hiller M 

PROVIDER: S-EPMC1903381 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature