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RNA Analysis Tools

• Riboswitch Finder
• RNAMOT: RNA Motif search program
• Transterm UTR Motif Search
• CARNAC: Secondary structure analysis of a family of
  homologous RNA
• DEQOR: Tool for Design and Quality Control of RNAi
• ERPIN: Easy RNA Profile IdentificatioN. Dev by Daniel Gautheret
  and Andre Lambert
• ILM: RNA Secondary Structure Prediction
• KineFold: RNA/DNA folding predictions
• MolMovDB: Database of Macromolecular Movements.
  By M. Gerstein, S. Flores, W. Krebs, N. Echols and others
• RNAfold: RNA Secondary Structure
• RNAsoft: Software for RNA/DNA secondary structure
  prediction and design. (University of British Columbia)
• Sfold: Folding and Design of Nucleic Acids
• siDirect
• siRNA Selection Server at WHITEHEAD
• siRNAdb
• TROD (T7 RNAi Oligo Designer): Designing of DNA
  oligonucleotides for the synthesis of short interfering RNAs (siRNAs)
  with T7 RNA polymerase.
• Vienna RNA Package: RNA Secondary Structure
  Prediction and Comparison
• RNAlishapes: A tool for RNA structure analysis based on aligned RNAs (Reference: Structural analysis of aligned RNAs. Nucleic Acids Res., 2006, Vol. 34, No. 19, pp. 5471-5481)

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