RNAshapes: an integrated RNA analysis package based on abstract shapes

Bioinformatics. 2006 Feb 15;22(4):500-3. doi: 10.1093/bioinformatics/btk010. Epub 2005 Dec 15.

Abstract

We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.

MeSH terms

  • Algorithms
  • Computer Graphics*
  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Pattern Recognition, Automated / methods
  • RNA / analysis
  • RNA / chemistry*
  • Sequence Analysis, RNA / methods*
  • Software*
  • Systems Integration
  • User-Computer Interface*

Substances

  • RNA