ivan-castro/rnatk-v0.2.0

RNAtk (RNA tool kit) focus on handle fasta files and RNA secondary/tertiary structures.

RNAtk - A python module to handle and analyze RNA sequences and its secondary and tertiary structures.

Copyright 2015 by Iván Castro

Version 0.2.0

Technical support: [email protected]

Installation in linux

$ wget https://github.com/Ivan-Castro/rnatk/archive/master.zip $ unzip rnatk-master.zip $ cd rnatk-master $ sudo python setup.py install

Python dependences

• RNA (http://www.tbi.univie.ac.at/RNA/)
• Bio (http://biopython.org/wiki/Main_Page)
• Numpy (http://www.numpy.org/)
• Scipy (http://www.scipy.org/)
• matplotlib (http://matplotlib.org/)
• moderna (http://genesilico.pl/moderna/)
• ete2 (http://pythonhosted.org/ete2/)
• pylab (http://wiki.scipy.org/PyLab)
• networkx (https://networkx.github.io/)

Other dependences

• Varna (http://varna.lri.fr/)
• muscle (http://www.drive5.com/muscle/)
• RNAview (http://ndbserver.rutgers.edu/)

Legal disclaimer

RNAtk is released under the GNU license, a copy of which is included in the distribution (/docs/copying.txt).

This software is provided "as-is". There are no expressed or implied warranties of any kind, including, but not limited to, the warranties of merchantability and fitness for a given application. In no event shall the authors be liable for any direct, indirect, incidental, special, exemplary or consequential damages (including, but not limited to, loss of use, data or profits, or business interruption) however caused and on any theory of liability, whether in contract, strict liability or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.

The authors take no responsibility for damage caused by this program or its components.

References

Some functions and processes are based on the following papers

• Schneider, T. D., Stormo, G. D., & Gold, L. 1986. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188: 415 - 431.
• Hofacker et al. 2002. Secondary Structure Prediction for Aligned RNA Sequences. J. Mol. Biol. 319: 1059-1066.
• Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids, Res. 32(5): 1792 - 1797.