Secondary Structure Prediction:

• Theory and Review Papers
  
  
  

Useful Softwares for the Predictions:

• MiRScan : miRNA Hairpin Scoring Tool
  1. MiRScan Homepage (in MIT, USA)
  2. Lab Homepage (in MIT, USA)
  3. Key Paper: Genes and Development 2003
  4. More Referece Paper Link
  
  
• MFold: RNA Sec. Str. Prediction Tool
  1. MFold Homepage (in RPI, USA)
  2. Lab Homepage (in RPI, USA)
  3a. Key Paper 1: NAR 2003 Zuker
  3b. Key Paper 2: JMB 1999 Mathews
  
  
• PseudoViewer: RNA Pseudo-Knot Structure Viewer
  1. PseudoViewer Homepage
  2. Biocomputing Lab in Inha University, KOREA
  3a. Key Paper 1: NAR 2003 Han
  3b. Key Paper 2: Bioinformatics 2002 Han
  3c. More Papers
  
  
• Human miRNA Str. Prediction Study by SNU Lab:
  2. BioIntelligence Lab in Seoul National University, KOREA
  3.Key Paper: NAR 2005
  
  
• FAM (Rfam & Pfam) : RNA and Protein DB
  1a. Rfam Homepage in Sanger Institute (UK)
  1b. Rfam Homepage in Washington Univeristy (USA)
  2a. Pfam Homepage in Sanger Institute (UK)
  2b. Pfam Homepage in Washington Univeristy (USA)
  3. Key Papers