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

@article{Hiller2006UsingRS,
  title={Using RNA secondary structures to guide sequence motif finding towards single-stranded regions},
  author={M. Hiller and Rainer Pudimat and Anke Busch and Rolf Backofen},
  journal={Nucleic Acids Research},
  year={2006},
  volume={34},
  pages={e117 - e117}
}
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… CONTINUE READING
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