[본문스크랩] RNA folding

http://www.bioinfo.rpi.edu/~zukerm/lectures/RNAfold-html/rnafold-html.html

• Introduction
  • What is RNA secondary structure?
  • Display of RNA Secondary Structures
• RNA Folding by Energy Minimization
  • Base pair dependent energy rules.
    • Fill and Traceback Example
  • Loop Dependent Energy Rules
    • What are loops?
    • Hairpin loops
    • Stacks, Bulges and Interior Loops
  • Algorithms for loop dependent rules
    • No single base stacking and constant energy for multi-branch loops.
    • Single base stacking and affine energies for multi-branch loops.
  • Suboptimal Algorithm
• The Equilibrium Partition Function
  • Counting foldings.
  • Partition functions.
    • Definition.
    • Algorithm for base pair dependent rules.
  • Heat Capacity and Melting
• Sample foldings
  • Simple Cases
    • Example 1
    • Example 2
  • Some real examples, good and bad.
    • The Potato Spindle Tuber Virus
    • E. coli 16S rRNA.
    • Folding E. coli and Zea Mays chloroplast 16S rRNA together.
    • Thermococcus celer, a ``well behaved'' Archaeon
  • Annotation of Foldings
• RNA Folding by Comparative Sequence Analysis
  • Examples
• Bibliography

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Michael Zuker Professor of Mathematical Sciences Rensselaer Polytechnic Institute 2003-06-25