RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints
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README.md

RNAblueprint library

Introduction

The RNAblueprint library solves the problem of stochastically sampling RNA/DNA sequences compatible to multiple structural constraints. It only creates sequences that fulfill all base pairs specified in any given input structure. Furthermore, it is possible to specify sequence constraints in IUPAC notation. Solutions are sampled uniformly from the whole solution space, therefore it is guaranteed, that there is no bias towards certain sequences.

The library is written in C++ with SWIG scripting interfaces for Python and Perl. Please cite the software as specified at the bottom of the page!

Dependencies

Required:

  • GNU Automake
  • Boost Graph Library
  • C++ Standard Library

Optional:

  • Boost Programm Options (default: on)
  • SWIG for interfaces (default: on)
  • Python for interface (default: on)
  • Perl for interface (default: on)
  • ExtUtils::Embed module for perl interface (default: on)
  • Doxygen for documentation
  • LaTeX for PDF documentation
  • libGMP for multiprecision integers
  • openmp for parallel computation
  • Boost Unit Test Framework

Installation

Just call these commands:

./autogen.sh
./configure
make
make install

In case of a local installation, please do not forget to adopt your path variables such as PATH, LD_LIBRARY_PATH, CPLUS_INCLUDE_PATH, PYTHONPATH, PERL5LIB

Most important configure options are:

--prefix Specify an installation path prefix
--with-boost Specify the installation directory of the boost library
--disable-program  Disable RNAblueprint program compilation
--disable-swig Disable all SWIG scripting interfaces
--enable-libGMP Enable the calculation of big numbers with multiprecision
--disable-openmp Disable the usage of parallel computation

TIP: You might want call ./configure --help for all install options!

Documentation

Library documentation is done using Doxygen. Call make doxygen-doc for a offline version in HTML and PDF. There is also a online version available here: http://viennarna.github.io/RNAblueprint/

Documentation of the RNAblueprint program is provided by calling RNAblueprint --help.

Testing

Unit tests are available for many functions of the library. Please call make check to run these tests!

How to cite

Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, and Sven Findeiß. “RNAblueprint: Flexible Multiple Target Nucleic Acid Sequence Design.” Bioinformatics, 2017. doi:10.1093/bioinformatics/btx263.