RNAz - predicting structural noncoding RNAs

Introduction

RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.

The method is described in:

Washietl S., Hofacker I.L., Stadler P.F.
Fast and reliable prediction of noncoding RNAs
Proc. Natl. Acad. Sci. U.S.A. 102: 2454-2459, 2005

RNAz 2.0: Improved noncoding RNA detection
Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF. Pac Symp Biocomput. 15:69-79, 2010

News

2011-10-06 RNAz version 2.1 is released. Some minor bug fixes and simplified command line options with more practical defaults. Also the documentation has been extended and updated.

2009-09-21 A pre-release of the new version 2.0 of RNAz is available. Among other additions, this new release features improved z-score estimates based on a dinucleotide model, a new classfication model built from a singificantly bigger test set and classfication model for structurally aligned sequences. The improvements are described in an upcoming Manuscript: Gruber et al. "RNAz 2.0: improved noncoding RNA detection" PSB 2010.

2008-04-07 A novel method to estimate the false discovery rate of RNAz is available. Instead of using a simplistic shuffling algorithm to randomize alignments, SISSIz simulates random alignments preserving dinucleotide content. The algorithm is described in this paper and the program can be downloaded here: http://sourceforge.net/projects/sissiz

2007-02-06 Our new RNAz web server is available here: rna.tbi.univie.ac.at/RNAz. It allows to analyze your sequences online without installing any software on your computer.

2006-10-13 RNAz 1.0 is available. A series of bugs have been fixed, most prominently the bug that caused the program to crash on 64 bit machines. If you are using a 64 bit machine make sure that you use the latest version! Thanks to all people who have reported bugs.

2006-03-28 A pre-release for the new version RNAz 1.0 is available. There are no major changes in the algorithm compared to the previous version. However, the user interface of RNAz has been improved. Most notably a set of Perl helper programs is available that implement a complete analysis pipeline suitable for large scale screens. See NEWS for a complete list of changes. Please note: I will call the current version ``pre-release" for a while just to make sure that I can fix potential bugs before I finally name it ``1.0". Also note the new Manual/Tutorial!

Download

VersionDateFilePlatformPackage type
2.1 10/06/2011 RNAz-2.1.tar.gz Linux/Unix/OSXSource
1.0 10/13/2006 RNAz-1.0-win32.msi Windows Binary

Old versions

The latest source code is available at https://github.com/wash/rnaz

Getting started

Linux / Unix / OSX

The following installation procedure should work on all Unix-like systems. On OS X it is necessary that you have installed the ``XCode" tools.

Download the latest RNAz-X.X-tar.gz and run the following commands:

tar -xzf RNAz-X.X-tar.gz
cd RNAz-X.X
./configure
make
make install

The last step requires root privileges and installs the RNAz files into the /usr/local/ tree. The executable is for example installed to /usr/local/bin and you should now be able to run the program which you can easily check by typing RNAz --version.

If you do not have root privileges on your system or prefer to install RNAz into a self-contained directory run configure for example like this:

./configure --prefix=/myhome/RNAz --datadir=/myhome/RNAz/share

The Perl programs are by default installed to /usr/local/share/RNAz/perl/. They are not installed by default since different people like their scripts in different locations. So copy all files from this directory to your favourite directory which is in your PATH of executables. For example copy them to /usr/local/bin:

cp /usr/local/share/RNAz/perl/* /usr/local/bin

Alternatively you can add this directory to your PATH.

MS Windows

Note: The windows support has been discontinued as of version 2.0. The windows package for version 1.0 is still available.

Simply download the latest RNAz-X.X-win32.msi file and double click it. Follow the instructions. Open a console window and type RNAz --version to test your installation.

The Perl programs are also automatically installed. To run them you need to have installed ActivePerl. Get the latest msi-installer package from www.activestate.com and follow the instructions. Make sure that you choose ``Add Perl to PATH environment variable" and ``Create Perl file extension association" during installation.

Testing RNAz

You can test RNAz on one of the example alignments (default location under Unix/Linux/OSX: /usr/local/share/RNAz/examples, Windows: c:\Program Files\RNAz\examples):

cd /usr/local/share/RNAz/examples
RNAz tRNA.aln

To test if the Perl programs work run for example:

rnazWindow.pl --window=120 --slide=40 unknown.aln | RNAz

Documentation

A manual/tutorial for using RNAz and helper programs is available here: manual.pdf

Manual pages are also available here:

Links

If you are interested in RNAz you might also be interested in ...

Contact

Please feel free to contact me for comments, bug-reports etc.

Stefan Washietl
Last modified: Thu Oct 06 2011