RNAHeliCes and HiKinetics

Abstract folding space analysis based on helices and RNA-kinetics based on folding space abstraction

Copyright (C) 2011-20 Jiabin Huang, Björn Voss. Send comments/bug reports to: J. Huang j.huang@uke.de.

Dependencies

RNAliHiKinetics needs RNAliHelices and RNAliHipath whose installation is described below. Additional dependencies are:

compile time:

• C++ compiler (for example GCC g++)
• C compiler (for example GCC)
• GNU make >= 3.81

compile time and runtime:

• Boost Libraries (>1.58): program_options, date_time (apt install libboost-all-dev)
• LAPACK

Installation

git clone https://github.com/huang/RNAHeliCes
autoreconf -f -i
./configure CFLAGS="-fno-stack-protector" CPPFLAGS="-std=c++98" CXXFLAGS="-std=c++98 -fno-stack-protector"
make
sudo make install

Notes:

• If there are any linking problems after installing, please add '/usr/local/lib' to LD_LIBRARY_PATH.

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

• ./src/libs/libRNA.a contains all Vienna package routines, this may be system dependent. If so, please reload this from Vienna RNA Package.
• If without SUPER privilege, use ./configure --with-boost-include-path="/your_path/boost_1_58_installed/include" --with-boost-lib-path="/your_path/boost_1_58_installed/lib" CFLAGS='-g -O2 -fno-stack-protector' CPPFLAGS='-std=c++98 -I/your_path/boost_1_58_installed/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2' CXXFLAGS='-std=c++98 -g -O2 -w -fno-stack-protector'

Test run

RNAHeliCes examples/collosoma_slrna.seq
HiPath -f examples/switches_4.faa -k 40 -P ./librna/vienna/rna_turner1999.par
HiTed examples/riboswitches.fas -t 1 -r 1

HiKinetics

See ./HiKinetics/README for HiKinetics.

Citations

[1] Huang, J., & Voß, B. (2011, September). RNAHeliCes—Folding Space Analysis Based on Position Aware Structure Abstraction. In German Conference on Bioinformatics, Weihenstephan, Germany (Vol. 79).

[2] Huang, J., Backofen, R., & Voß, B. (2012). Abstract folding space analysis based on helices. RNA, 18(12), 2135-2147.

[3] Huang, J., & Voß, B. (2012, September). Reducing the search space in RNA helix based folding. European Conference on Computational Biology 2012. European Conference on Computational Biology (ECCB) 2012.

[4] Huang, J., & Voß, B. (2014). Analysing RNA-kinetics based on folding space abstraction. BMC bioinformatics, 15(1), 60.