RNA analysis

• MFOLD: prediction of RNA Secondary Structure by Energy Minimization (Zuker) (advanced form)
• Vienna RNA package (documentation)
  • RNAfold: calculate secondary structures of RNAs (advanced form)
  • RNAeval: calculate energy of RNA sequences on given secondary structure (advanced form)
  • RNAheat: calculate specific heat of RNAs (advanced form)
  • RNAdistance: calculate distances of RNA secondary structures (advanced form)
  • RNApdist: calculate distances of thermodynamic RNA secondary structures ensembles (advanced form)
  • RNAinverse: find RNA sequences with given secondary structure (advanced form)
  • RNAsubopt: calculate suboptimal secondary structures of RNAs (advanced form)
• tRNAscan-SE: detection of transfer RNA genes (advanced form)
• FAStRNA: predicts potential tRNA genes in genomic DNA sequences. FAStRNA-CM relies on a probabilistic model. FAStRNA-CLASS relies on a pattern-matching approach.
• palindrome: Looks for inverted repeats in a nucleotide sequence (EMBOSS).
• RNAGA: Prediction of common secondary structures of RNAs by genetic algorithm (Chen, Le, Maizel)
• sirna: Finds siRNA duplexes in mRNA (EMBOSS).