GERF Bulletin of Biosciences 2010, 1(1): 51-54

Software Review

Mfold©: RNA modeling program

Authors: Prof: Michael Zuker, Professor of mathematical sciences;
License: Freeware, Copyright © Washington University.
Reviewed By: Dr. Ahmed Mansour Alzohairy
Genetic Department, Faculty of Agriculture, Zagazig University, Egypt.

Mfold at a glace journals, Mfold become very important bioinformatics

RNA structure is very important in many biological
processes, including translation regulation in messenger
RNA and replication of single-stranded RNA viruses. Much
of Michel Zuker work is on studying RNA structure. He
developed Mfold program as tool for predicting the secondary
structure of RNA, mainly by using thermodynamic methods
(the Gibbs free energy). That sophisticated RNA modeling
program takes into account many parameters, (e.g. pH,
temperature, and the local composition bias of RNA), that
affect the RNA folding. Using thermodynamics in the
prediction algorithm of RNA structure is not common with
Single sequence secondary structure prediction software.
Up till now, only three programs, (Mfold, RNA fold,
RNAshapes), is known to use this feature (Table 1). Recently,
Mfold has been replaced by UNAFold, a software package
that is much easier to install and run and it offers many more
types of computations.
Mfold History
SantaLucia (1998) have published his work on the unified
view of polymer, dumbbell, and oligonucleotide DNA
thermodynamics in PNAS journal. That paper was the base
for M. Zuker (1999) and his colleagues to study the expanded
sequence dependence of thermodynamic parameters for the
prediction of RNA secondary Structure. Since then, Zuker
has worked extensively to develop mfold, a program for
predicting the secondary structure of RNA and DNA, mainly
by using thermodynamic methods, which was published at
Nucleic Acids Research journal in 2003 (Chain, 2005).
Mfold contribution to research
Many researchers in the field of Molecular biology have
used using thermodynamics based Mfold modules during
their original research for predicting the secondary structure
of RNA and DNA. With many citations in peer reviewed
software in molecular biology for prediction of secondary
RNA structure. The freeware license and its efficient up to
date modules beside its quick ability to produce results make
it one of the most popular programs predicting secondary
structure of RNA of nowadays.
Advantages and Disadvantages of Mfold
Advantages
- Mfold is very easy to use and free of charge online.
- Mfold is internet based program that runs on
(almost) any computer that has access to the
Internet.
- Mfold has many versions and updated regularly.
Disadvantages:
- The energetic model that Mfold uses ignores 3-D
interactions or protein-RNA interactions that could
stabilize a suboptimal fold.
- Prediction from Mfold does not always correspond
to the true biological fold of the RNA. So that, the
researcher should be able to make his own decision.
- The researcher should be able to judge the stability
of the optimal fold when Mfold returns suboptimal
models.
- You cannot force pseudo-knots in Mfold.
- The time Mfold needs to analyze sequences
increases very rapidly with their length.
Software Design
Mfold can predict the energetically optimal secondary
structure of an RNA molecule by using of Zuker algorithm.
Versions 3.xxx of Mfold for Unix and Linux operating systems
are available via a free license for academic and nonprofit
use only; commercial use is available for a fee.

*Corresponding author: alzohairy@yahoo.com

www.gerfbb.com
GERF Bulletin of Biosciences 2010, 1(1): 51-54 52

Name Description Links References

Secondary structure prediction based on generalized http://www.ncrna.or Hamada et al.
CentroidFold
centroid estimator g/centroidfold/ (2009)
Secondary structure prediction method based on http://contra.stanfor Do CB et al.
conditional log-linear models (CLLMs), a flexible d.edu/contrafold/ser (2006.
CONTRAfold class of probabilistic models which generalize upon ver.html
feature- by using discriminative training and SCFGs
scoring.rich
Secondary structure prediction method based on http://cylofold.abcc. Bindewald et al.,
CyloFold placement of helices allowing complex ncifcrf.gov/ 2010
pseudoknots.
Folding kinetics of RNA sequences including http://kinefold.curie Xayaphoummin
KineFold pseudoknots by including an implementation of the .fr/cgi-bin/form.pl e A, et al. 2005,
partition function for knots. 2003
http://frontend.bioin Zuker and
fo.rpi.edu/applicatio Stiegler, 1981
Mfold MFE RNA structure prediction algorithm.
ns/hybrid/quikfold.
php
http://bibiserv.techf Reeder et al.,
A dynamic programming algorithm for the ak.uni- 2007
PknotsRG
prediction of a restricted class of RNA pseudoknots. bielefeld.de/pknotsr
g/submission.html
http://rna.tbi.univie. Hofacker et al.,
ac.at/cgi- 1994, McCaskill
bin/RNAfold.cgi 1990, Hofacker
MFE RNA structure prediction algorithm. Includes and Stadler
an implementation of the partition function for 2006,
RNAfold
computing basepair probabilities and circular RNA Bompfünewerer
folding. 2008)

MFE RNA structure prediction based on abstract http://bibiserv.techf Giegerich et

shapes. Shape abstraction retains adjacency and ak.uni- al.,2004, Voß et
nesting of structural features, but disregards helix bielefeld.de/rnashap al., 2006
lengths, thus reduces the number of suboptimal es/
RNAshapes
solutions without losing significant information.
Furthermore, shapes represent classes of structures
for which probabilities based on Boltzmann-
weighted energies can be computed.
A program to predict lowest free energy structures http://rna.urmc.roch Mathews et al.
and base pair probabilities for RNA or DNA ester.edu/RNAstruc 2004,
sequences. Structure prediction can be constrained ture.html Mathews 2004
using experimental data, including SHAPE,
enzymatic cleavage, and chemical modification
RNAstructure
accessibility. Graphical user interfaces are available
for Windows and for Mac OS-X/Linux. Programs
are also available for use with Unix-style text
interfaces. Additionally, a C++ class library is
available.
http://sfold.wadswo Ding and
Statistical sampling of all possible structures. The rth.org/cgi- Lawrence 2003,
Sfold sampling is weighted by partition function bin/index.pl Ding et al. 2004,
probabilities. 2005, Chan et
al. 2005
Table: 1. Comparative table for other online for RNA Single sequence secondary structure prediction.

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53
Limitation
The current limit of the server is 3,000 bases. This is
convenient for most non-coding RNAs except the largest
ribosomal ones
Mfold availability online
Servers in USA:
- www.bioinfo.rpi.edu/applications/mfold/.
- http://frontend.bioinfo.rpi.edu/applications/mfold/
cgi-bin/rna-form1.cgi
- http://mfold.bioinfo.rpi.edu/cgi-bin/rna-form1.cgi
European mirrors of mfold:
- bibiserv.techfak.uni-bielefeld.de/cgi-bin/
mfold_submit
- bioweb.pasteur.fr/seqanal/interfaces/mfold-
simple.html
Australian counterpart:
- mfold.burnet.edu.au
References
1. Bindewald E, Kluth T and Shapiro BA (2010).
CyloFold: secondary structure prediction including
pseudoknots. Nucleic Acids Research Suppl (W):
368-72.
2. Bompfünewerer AF, Backofen R, Bernhart SH, et
al. (2008). Variations on RNA folding and alignment:
lessons from Benasque. J Math Biol., 56 (1-2): 129–
144.
3. Chan CY, Lawrence CE and Ding Y (2005). Structure
clustering features on the Sfold Web server.
Bioinformatics 21 (20): 3926–8.
4. Ding Y, Chan CY and Lawrence CE (2004). Sfold
web server for statistical folding and rational design
of nucleic acids. Nucleic Acids Res. 32 (Web Server
issue): W135–41.
5. Ding Y, Chan CY and Lawrence CE (2005). RNA
secondary structure prediction by centroids in a
Boltzmann weighted ensemble. RNA 11 (8): 1157–
66.
6. Ding Y and Lawrence CE (2003). A statistical
sampling algorithm for RNA secondary structure
prediction. Nucleic Acids Res. 31 (24): 7280–301.
GERF Bulletin of Biosciences 2010, 1(1): 51-54
7. Do CB, Woods DA and Batzoglou S (2006).
CONTRAfold: RNA secondary structure prediction
without physics-based models. Bioinformatics 22
(14): 90–8
8. Giegerich R, Voß Band Rehmsmeier M (2004).
Abstract shapes of RNA. Nucleic Acids Res. 32
(16): 4843–4851.
9. Hofacker IL, Stadler PF (2006). Memory efficient
folding algorithms for circular RNA secondary
structures. Bioinformatics 22 (10): 1172–6.
10. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S,
Tacker M and Schuster P (1994). Fast Folding and
Comparison of RNA Secondary Structures.
Monatshefte f. Chemie 125: 167–188.
11. Markham NR and Zuker M (2008). UNAFold:
software for nucleic acid folding and hybridization.
Methods Mol. Biol 453: 3–31.
12. Mathew DH. Sabina J, Zuker M and Turner DH
(1999). Expanded Sequence Dependence of
Thermodynamic Parameters Improves Prediction of
RNA Secondary Structure J. Mol. Biol. 288, 911-
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13. Mathews DH (2004). Using an RNA secondary
structure partition function to determine confidence
in base pairs predicted by free energy minimization.
RNA 10 (8): 1178–1190.
14. Mathews DH, Disney MD, Childs JL, Schroeder SJ,
Zuker M and Turner DH (2004). Incorporating
chemical modification constraints into a dynamic
programming algorithm for prediction of RNA
secondary structure, Proceedings of the National
Academy of Sciences, USA. 101 (19): 7287–7292.
15. McCaskill JS (1990). The equilibrium partition
function and base pair binding probabilities for RNA
secondary structure. Biopolymers. 29 (6-7): 1105–
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16. Michiaki Hamada, Hisanori Kiryu, Kengo Sato,
Toutai Mituyama and Kiyoshi Asai (2009).
Predictions of RNA secondary structure using
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GERF Bulletin of Biosciences 2010, 1(1): 51-54 54

generalized centroid estimators. Bioinformatics. 25

(4): 465–473.

17. Reeder J, Steffen P and Giegerich R (2007).

pknotsRG: RNA pseudoknot folding including near-
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Acids Res. 35 (Web Server issue): W320–4.

18. SantaLucia, JJr (1998) A unified view of polymer,

dumbbell, and oligonucleotide DNA nearest-
neighbor thermodynamics. Proc. Natl. Acad. Sci.
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19. Voß B, Giegerich R and Rehmsmeier M (2006).

Complete probabilistic analysis of RNA shapes.
BMC Biology. 4: 5.

20. Xayaphoummine A, Bucher T and Isambert H

(2005). Kinefold web server for RNA/DNA folding
path and structure prediction including
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21. Xayaphoummine A, Bucher T, Thalmann F and

Isambert H (2003). Prediction and statistics of
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22. Zuker M and Stiegler P (1981). Optimal computer

folding of large RNA sequences using
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folding and hybridization prediction. Nucleic Acids
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www.gerfbb.com