sibRNAfold project

Background

The sibRNAfold project is based on Vienna RNAfold, which is a program for RNA secondary structure prediction through energy minimization. Vienna RNAfold was written by Ivo Hofacker, Walter Fontana, Sebastian Bonhoeffer and Peter Stadler at the University of Vienna. Both programs, sibRNAfold and Vienna RNAfold, are based on a dynamic programming algorithm for minimum free energy structure prediction (Zuker & Stiegler 1981) which yields a single optimal structure.
Here is the page describing Vienna RNAfold, and here is the original source code.

Purpose

SibRNAfold implements a modification of the dynamic programming algorithm that significantly speeds up the minimum free energy calculations, while producing identical result as Vienna RNAfold. As such it achieves the following main goals:

speed improvement
extends the application range of RNA folding to longer sequences
it is compatible with existing sequence analysis pipelines

A manuscript describing the modified algorithm is currently under preparation. Below are some real sequences used for testing and comparison of the execution time required for finding the secondary structures for both programs:

	Vienna RNAfold	sibRNAfold
HIV genome	344 sec	19 sec
SARS CoV genome	10'304 sec	348 sec
Human Titin mRNA	N/A*	4 hrs

(*) The estimated execution time for the hs_titin sequence using Vienna RNAfold is several days. However the current Vienna RNAfold version does not support folding of sequences longer than 32k nts. The sequences are run on a server machine with 64GB RAM, which is the required memory for folding a sequence with ~100k nt length. Both programs were tested with the parameter maxloop set to 10 (instead of the default value of 30) and option -d2, in order to better analyze the effects of the cubic computational step.

Status

The name was chosen to denote the fact the sibRNAfold is a derivative work from Vienna RNAfold. SIB stands for the Swiss Institute of Bioinformatics. The current version of the sibRNAfold code is developed by Slavica Dimitrieva and Philipp Bucher at the School of Life Sciences at EPFL in Lausanne. Both are also members of the Swiss Institute of Bioinformatics.

The sibRNAfold project is kindly hosted by SourceForge here.

The current version of sibRNAfold is 1.0. Installation instructions are available here. Users comments are welcome.