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

摘要: RNA binding proteins recognize targets in a sequence specific manner. Apart from the sequence, secondary structure context of site also affects affinity. Binding sites are often located single-stranded regions and it was shown that sequestration motif double-strand abolishes protein binding. Thus, is desirable to include knowledge about structures when searching for protein. We present approach MEMERIS motifs set sequences simultaneously integrating information structures. To abstract structural elements, we precompute position-specific values measuring single-strandedness all substrings an sequence. These used as prior starts guide search. Extensive tests with artificial biological data demonstrate able identify even if stronger parts exists. The discovered occurrences datasets mostly coincide known protein-binding sites. This algorithm can be finding RNA-binding SELEX or other data.