RNAblueprint

RNAblueprint is a C++ library implementing a graph coloring approach to sample sequences compatible with structural and sequence constraints stochastically. This approach allows for efficient and uniform sampling and can be combined with any other software package for diverse RNA design applications. We also created scripting interfaces to adapt existing code easily and provided example Python implementations and benchmark datasets.

Topic

Nucleic acids;Data visualisation;RNA

Detail

  • Operation: Nucleic acid design

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.3.2

  • Credit: The Future and Emerging Technologies (FET) programme within the Seventh Framework Programme for Research of the European Commission, the COST-Action CM1304 Systems Chemistry, the FWF projects SFB F43 RNA regulation of the transcriptome and Doktoratskolleg RNA Biology.

  • Input: -

  • Output: -

  • Contact: s.hammer@univie.ac.at, ivo@tbi.univie.ac.at, sven@tbi.univie.ac.at

  • Collection: -

  • Maturity: -

Publications

  • RNAblueprint: flexible multiple target nucleic acid sequence design.
  • Hammer S, et al. RNAblueprint: flexible multiple target nucleic acid sequence design. RNAblueprint: flexible multiple target nucleic acid sequence design. 2017; 33:2850-2858. doi: 10.1093/bioinformatics/btx263
  • https://doi.org/10.1093/bioinformatics/btx263
  • PMID: 28449031
  • PMC: PMC5870862

Download and documentation

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