MASTR

MASTR (Multiple Alignment of STructural RNAs) is a software tool that simultaneously predicts the structure and aligns multiple RNA sequences. The algorithm uses Markov chain Monte Carlo in a simulated annealing framework to minimize a combined cost function that considers sequence conservation, covariation, and basepairing probabilities. MASTR is competitive with similar programs in terms of accuracy and computational efficiency.

Topic

Sequence analysis

Detail

  • Operation: Multiple sequence alignment;RNA secondary structure prediction

  • Software interface: Command-line user interface;Web user interface

  • Language: -

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: The Novo Scholarship Program, the Carlsberg Foundation and the Danish National Research Foundation.

  • Input: FASTA

  • Output: -

  • Contact: stinus@binf.ku.dk

  • Collection: -

  • Maturity: -

Publications

  • MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
  • Lindgreen S, et al. MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. 2007; 23:3304-11. doi: 10.1093/bioinformatics/btm525
  • https://doi.org/10.1093/bioinformatics/btm525
  • PMID: 18006551
  • PMC: -

Download and documentation

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