REAPR: Realignment for Prediction of Structural Non-coding RNA

Installation Instructions

REAPR runs with python v2.7 or higher. No other compilation is required, except REAPR depends on several software packages. To install REAPR in a UNIX-like (e.g. GNU/Linux or MacOS X) environment, please follow these simple instructions:
  1. Install the ViennaRNA package (at least version 2.0.5) (Download Vienna RNA package).

  2. Install RNAz 2.0 or higher (Download RNAz)

  3. Install LocARNA
    4. Download the LocARNA source (locarna-1.7.1.tar.gz). Then, compile and install by running the following commands from a terminal:

    tar xzf locarna-1.7.1.tar.gz
    cd locarna-1.7.1

    ./configure --enable-librna
    make
    make install

    If the Vienna package is installed in a non-standard path, the path should be specified by adding the option --with-vrna="path/to/ViennaRNA-2.0.x" with appropriate path when calling configure. With configure option --prefix="locarna/installation/path" one can specify a non-standard installation path for LocARNA. Other available configure options are reported by "./configure -h".

  4. Download reapr.zip. Extract the contents into a directory by running the command

    unzip reapr.zip

    or by using your preferred zip archive tool. Configure the REAPR scripts to know the location of other required software packages by running the command

    python configure.py [options]

    Run REAPR on a whole genome alignment with the command

    python REAPR.py [options]

    To see a list of options for configure.py and REAPR.py, run them with the '--help' option. Please refer to the included README for further details on configuring and using REAPR, formatting the input to REAPR.py, and a description of output files.

  5. To test that REAPR and all packages were installed correctly, we have provided a portion of the whole genome alignment of 12 Drosophila species used in this study at test-WGA.zip. Extract the contents into a directory, change into the directory, and run REAPR on the WGA with the following command

    python /path/to/REAPR.py -a wga_alignments -s species -g dro_tree -d 5 10 20 -p 2 -r /dev/shm --alistat --compalignp

    REAPR will realign using LocARNA with limited deviations of delta = 5, 10, and 20. LocARNA will also use the tree in 'dro_tree' to guide progressive alignment. Temporary files will be written to a RAM disk at '/dev/shm' for efficiency. Finally, REAPR will output a table 'summary.tab' that summarizes the RNAz scores before and after realignment, sequence identities of alignments (computed by alistat), and the amount of realignment change (computed by compalignp). Two CPU cores will be used for computation. This command may take 5 or more minutes to run, depending on your system.