Pankov: Probabilistic Sankoff-like simultaneous alignment and folding of RNAs inspired by Markov chains

This is the Pankov repository for structural alignment of RNAs, which is an extended branch of LocARNA package.

Installation

This branch is planned to be merged into the main LocARNA repository, on a long term. Please refer to README.txt and INSTALL files to follow the detailed installation instruction.

Quick guide

1. Make sure autotools dependencies are installed and run: libtoolize && aclocal && autoheader&& automake -a -c && autoconf

2. Make sure Vienna RNA tools are installed and run the make configuration: ./configure --with-vrna=PATH_TO_VIENNA RNA

3. Then run make

Usage

After installation you can run Pankov binary file pankov from the bin directory in the installation path or the src directory. Please always pass these parameters to use Pankov which uses the conditional probably --track-closing-bp --use-cond, the parameters are mandatory for the proper run of the program.

Call example: ./src/pankov seqA.fa seqB.fa --write-structure --track-closing-bp --use-cond

Further info can be found using --help option as well as the LocARNA package documentation.