Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction
 Stefan Janssen^{1},
 Christian Schudoma^{2},
 Gerhard Steger^{3}Email author and
 Robert Giegerich^{1}Email author
https://doi.org/10.1186/1471210512429
© Janssen et al; licensee BioMed Central Ltd. 2011
Received: 10 June 2011
Accepted: 3 November 2011
Published: 3 November 2011
Abstract
Background
Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate nearoptimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of structures and shapes. Although all programs refer to the same physical model, they implement it with considerable variation for different tasks, and little is known about the effects of heuristic assumptions and model simplifications used by the programs on the outcome of the analysis.
Results
We extract four different models of the thermodynamic folding space which underlie the programs RNAFOLD, RNASHAPES, and RNASUBOPT. Their differences lie within the details of the energy model and the granularity of the folding space. We implement probabilistic shape analysis for all models, and introduce the shape probability shift as a robust measure of model similarity. Using four data sets derived from experimentally solved structures, we provide a quantitative evaluation of the model differences.
Conclusions
We find that search space granularity affects the computed shape probabilities less than the over or underapproximation of free energy by a simplified energy model. Still, the approximations perform similar enough to implementations of the full model to justify their continued use in settings where computational constraints call for simpler algorithms. On the side, we observe that the rarely used level 2 shapes, which predict the complete arrangement of helices, multiloops, internal loops and bulges, include the "true" shape in a rather small number of predicted high probability shapes. This calls for an investigation of new strategies to extract high probability members from the (very large) level 2 shape space of an RNA sequence. We provide implementations of all four models, written in a declarative style that makes them easy to be modified. Based on our study, future work on thermodynamic RNA folding may make a choice of model based on our empirical data. It can take our implementations as a starting point for further program development.
Keywords
Background
Motivation
A wide variety of bioinformatics tools exist, which help to analyze RNA secondary structure based on an experimentally supported, thermodynamic model of RNA folding [1]. Typical tasks performed by such tools are

prediction of a single, "optimal" structure of minimal free energy,

computation of nearoptimal structures, either by complete enumeration up to a certain energy threshold, or by sampling from the folding space,

computation of base pair probabilities and dot plots,

computation of representative structures of different abstract shapes, or

computation of Boltzmann probabilities, either of individual structures, or accumulated over all structures of the same abstract shape.
From a macroscopic point of view, all these approaches are based on the same thermodynamic model, but when checking in detail, this does not hold. Algorithms for different tasks make certain assumptions about the folding space, where little is known to which extent these assumptions influence the outcome of the analysis.
The present study is designed to fill this gap. We explicate the details of four different models of the RNA folding space, named NoDangle, OverDangle, MicroState and MacroState. They capture four different models of the folding space, as they are implemented in the programs RNAFOLD[2], RNASHAPES[3], and RNASUBOPT[4].^{1} We compare the outcome of predictions from the different models, and evaluate them against three data sets derived from experimentally proved structures.
Goals of the evaluation
The goal of this study is not to define a "correct" or "best" way of modeling the RNA folding space. Different definitions may retain their merits in the light of different computational constraints. We want to explicate the differences in the results which are due to the choice of a particular model. Aside being interesting in its own right, this allows future algorithms designers to make a wellfounded choice of the model they base their work on.
How to compare the performance of different models? A first idea would be to evaluate them with respect to prediction of the structure of minimum free energy (MFE; for details see below), using a reference set of trusted structures. This has been done occasionally [1, 5], and we will include such an evaluation here for the sake of completeness. However, MFE structure prediction is notorious in the sense that a slight offset in energy can lead to a radically different structure. This is a consequence of the underlying thermodynamic model, and not due to its inadequate implementation. For a more robust evaluation, we need a measure which constitutes a more comprehensive characteristic of the overall folding space of an RNA molecule, including evidence for competing nearoptimal structures of significant structural variation.
Abstract shapes of RNA [3, 6] provide such a measure. This approach provides two essential types of analysis: (1) to compute a handsome set of representative, nearoptimal structures, which are different enough to be of interest, and (2) to compute shape probabilities, which accumulate individual Boltzmann probabilities over all structures of the same shape. The shape probability is a robust measure of structural welldefinedness, and in contrast to folding energy, it is independent of base composition and meaningful for comparing foldings of different sequences with similar length.
Types (1) and (2) of abstract shape analysis are achieved by different algorithms, using different models of the folding space, in the program RNASHAPES. A similar situation prevails within the Vienna RNA package, where different models of the folding space are used with various functions of RNAFOLD and RNASUBOPT under different parameter settings.
For our evaluation, we implement probabilistic shape analysis in four different ways, three of which closely correspond to the folding space models implemented for MFE prediction in RNAFOLD^{2}, and two of which correspond to the algorithms used in RNASHAPES. This set of programs will allow us to derive observations about the underlying folding space models.
Methods
In this section, we recall the definitions underlying the thermodynamic model of RNA folding, and then proceed to specify four different implementations of this model.
The thermodynamic model
Free energy and partition function
The structure of lowest free energy is called the (thermodynamically) optimal structure or structure of minimum free energy (MFE).
where matched parentheses indicate a base pair and dots indicate unpaired bases.
Abstract shapes
Both shapes indicate that the structure is a socalled Yshape, a multiloop with a twoway branch. This most abstract view is conveyed by abstraction level 5. The less abstract level 2 shape indicates, in addition, that the outer stem is interrupted by a bulge on the 5' side, and that the 3' branch inside the multiloop is interrupted by an internal loop. For a detailed definition of shape abstraction levels, see [9].
Implementing the basic energy model  no dangling bases
Elementary functions in the basic thermodynamic energy model
Function  Description 

sr _energy  The most important source for stabilizing an RNA secondary structure is stacking of two (or more) base pairs. 
termau _energy  A base pair A:U at the terminal end of a stacking region adds less stabilizing energy than within a stacking region. 
hl _energy  Stabilizing contribution for the loopclosing base pair stack plus destabilizing contribution for the hairpin loop region plus bonus energy for special loop sequence (e. g. extrastable tetra loops). 
bl _energy  Analog to hl _energy, but for a destabilizing loop region bulged out to the left. 
br _energy  Symmetric case to bl _energy. 
il _energy  Analog to hl _energy, but with two destabilizing loop regions. 
ml _energy  Since a multiloop of x stems is less stable than x adjacent stems, it gets a penalty. 
ul _energy  Each stem in a multiloop gets an initial penalty. 
ss _energy  Regions of unpaired bases could get penalized, but we set this value to zero. 
sbase _energy  Same as ss _energy, but for a single unpaired base. 
Implementing the full energy model  with dangling bases
In addition to the basic energy model described above, unpaired bases at the end of a helix can stabilize the helix by stacking on the terminal base pair [11–13]^{3}.
and 31 more. Each end of a helix can have dangling bases, except an end which leads to the hairpin loop. In this case, energy contributions from dangling bases are already incorporated in the energy parameters for the loops.
Given a concrete secondary structure, it is no problem to consider all possible dangles and compute the optimal energy for this structure. The program RNAEVAL from the Vienna Package can be used for this purpose. However, for structure prediction from a primary RNA sequence, dangle means trouble, as we shall see shortly.
Modeling folding spaces with tree grammars
Tree representation of structures
All approaches using the thermodynamic model are implemented via dynamic programming. Recursively, structures are composed from smaller substructures. Such a dynamic programming algorithm always has an underlying grammar, which describes all the candidates in the folding space of a given RNA sequence. Hence, by extracting the grammars behind different algorithms, we can analyze the differences in their respective folding space in a precise way, and without obscuring implementation detail.
The grammars we use are tree grammars. Nonterminal symbols designate different components of secondary structure, such as a stacking region or a bulge loop. Function symbols in the tree grammar are used to indicate how structures are built up from smaller components. For example, a snippet of a tree structure such as shown in Figure 1 designates at its bottom an unpaired stretch of one or more bases (r), 5' of a closed substructure of any type. This situation is indicated by the function symbol bl, which stands for "bulge left". The unpaired stretch and the substructure is surrounded by two stacking (C:G) base pairs, and enclosed in yet another base pair, added by function sr, which extends a "stacking region". These functions can be seen as actual constructors of a treelike data structure, representing secondary structures. They can (and will) also be seen as functions, which all call upon the energy functions of the thermodynamic model, to compute either free energies or their corresponding Boltzmann weights. We can also interpret them as functions which count base pairs in the structure they build, or compose the dotbracket string for that structure, compute their abstract shape, and so on. Modeling structures as trees built from functions that can be interpreted in different ways provides a uniform and flexible formalism for many purposes.
From tree grammars to folding algorithms
Tree grammars modeling the folding space of RNA essentially constitute executable code. They can be literally transcribed into a language supporting the algebraic dynamic programming technique [14]. We use the language GAPL as provided in the recent Bellman's GAP programming system [15, 16]. This approach is essential for the study at hand. It takes from us not only the burden to implement and debug dynamic programming recurrences for each of the four algorithms. It also guarantees that the different algorithms correctly implement their respective models, share the energy model, are implemented with the same degree of optimization, and are independent of the programming skills of a bunch of graduate students.
Grammars and their relation to established structure prediction programs
We will present four grammars, NoDangle, OverDangle, MicroState and MacroState. The first three implement the folding space of RNAFOLD used with options d0, d2, and d1, respectively. The grammars MicroState and MacroState implement the folding space of RNASHAPES in its two functions. All four grammars will then be empowered with shape abstraction, and are used in our evaluation for computing shape probabilities under the different models.
Energy functions for dangling bases
Function  Description 

dl _energy  A single base left of a closed substructure can dangle onto this stack and thus might further stabilize it. 
dr _energy  Symmetric case to dl _energy. 
ext _mismatch _energy  Two bases left and right of a stack, which do not form a basepair (they mismatch), can dangle from both sides to the stack. 
dli _energy  A multiloop is closed by one stack. A single base at the inside of the multiloop and directly next to the closing stack might dangle from left onto this stack. The energy values are the same as dr _energy, but for a reversed subsequence. 
dlr _energy  Symmetric case to dli _energy. 
ml _mismatch _energy  Two bases on both inner sides of a multiloop closing stack may dangle from inside onto this stack, but do not form a basepair (mismatch). 
Crossreference between the energy functions in our programs, and which energy contributions (model functions) they call upon.
Function  Used in evaluation function  

NoDangle  OverDangle  MicroState  MacroState  
termauenergy  ml  ml  ml  ml 
mldl  mldl  
mldr  mldr  
mldlr  mldlr  
mladl  
mladr  
mladlr  
mldladr  
mladldr  
drem  drem  drem  drem  
edl  edl  
edr  edr  
edlr  edlr  
dl _energy  edl  edl  
ambd  
ambd'  
acomb  
mladl  
mladlr  
mladldr  
dr _energy  edr  edr  
ambd  
ambd'  
acomb  
mladr  
mladlr  
mldladr  
ext_mismatch_energy  drem  edlr  edlr  
dli _energy  mldl  mldl  
mldladr  
mladl  
mladlr  
mladldr  
dri _energy  mldr  mldr  
mladldr  
mladr  
mladlr  
mldladr  
ml_mismatch_energy  ml  mldlr  mldlr  
sr _energy  sr  sr  sr  sr 
hl  hl  hl  hl  
bl  bl  bl  bl  
br  br  br  br  
il  il  il  il  
ml  ml  ml  ml  
mldl  mldl  
mldr  mldr  
mldlr  mldlr  
mladldr  
mladr  
mladl  
mladlr  
mldladr  
hl_energy  hl  hl  hl  hl 
bl_energy  bl  bl  bl  bl 
br_energy  br  br  br  br 
il_energy  il  il  il  il 
ml_energy=3.4  ml  ml  ml  ml 
mldl  mldl  
mldr  mldr  
mldlr  mldlr  
mladlr  
mldladr  
mladldr  
mladr  
mladl  
ul_energy=0.4  incl  incl  incl  incl 
ml  ml  ml  ml  
ssadd  
ss_energy=0  addss  addss  addss  addss 
ssadd  
sbase_energy=0  sadd  sadd  sadd  sadd 
Model NoDangle
NoDangle is our grammar incorporating the elementary energy model, without considering dangling bases at all. It corresponds to the model underlying RNAFOLD when used with option noLP d0^{4}. It is also used in RNASUBOPT. We give a narrative explanation of how this grammar works.
A closed substructure is a stack of base pairs which eventually leads to one of five structural motifs: hairpin loop (hairpin), bulge to the left (leftB), bulge to the right (rightB), internal loop (iloop) or multiloop. The multiloop is a concatenation (ml _comps and ml _comps1) of two or more substructures, embraced by one closing stack. Note that all motifs have at least two closing base pairs which form a stack. This implements the convention of disallowing lonely pairs. The helix initiated by two closing pairs can be elongated by sr. A region (r) is a nonempty stretch of unpaired bases (b), whose length can be further constrained, e. g. to be at most 30 bases (r30) for internal loops or at least 3 bases (r3) for a hairpin loop.
The algebra functions drem and ml control the dangling behavior, which is the only difference between NoDangle and OverDangle. In NoDangle, they do not make any dangling energy contributions at all.
Model OverDangle
OverDangle is the grammar which considers dangling base energies in a simplified form. It corresponds to RNAFOLD called with options noLP d2^{5}. The grammar itself is identical to NoDangle (cf. Figure 2). It computes the same folding space, but evaluates energies differently. It assumes an energy contribution from dangling bases on every side of a helix, even if a base is not available for dangling, for example because it is itself engaged in another helix, or already dangling there. The algebra functions drem and ml control the dangling behavior, which is the only difference between NoDangle and OverDangle. In OverDangle drem and ml always adds dangling energies for left and right dangles. This is why the production using drem uses two loc symbols: loc recognizes the empty word, and returns its position in the sequence. These positions are used by drem to look at the two bases to the left and right of the closed substructure.
This "overdangling" model is used because a correct treatment of dangles is much more complicated, as we shall see below. As a plausibility argument in favor of this heuristic, one may say that when a base is overdangled, for example between two adjacent helices, as with the midpoint in "((...)).((...))", this can be seen as a bonus for coaxial stacking of the two helices. Including full coaxial stacking could be considered as a further refinement of the folding space beyond the MicroState model, which will be described below. Still, due to overdangling, the MFE energy value computed may be smaller than actually assigned by the thermodynamic model to the underlying structure. Partition function computations in RNAFOLD use the OverDangle approach, and so does RNASUBOPT with option d2 (and even d1, but see below).
Would we use both NoDangle and OverDangle to produce a list of all structures in the folding space, sorted by free energy, these lists would hold the same structures, but in a different order. The true MFE structure (under the full model with correct dangles) will be near the front of each list, but it is not guaranteed to come out on first place. Our next two grammars are designed to achieve this goal.
Model MicroState
Grammar MicroState is a grammar which refines our model of a secondary structure. It corresponds to RNAFOLD noLP d1^{6} and is used in the 2004 release of RNASHAPES[3] for the computation of representative structures of different shape.
All variants of the same secondary structure, augmented with different dangles, are now separate members of the folding space. In contrast to the classical model, accounting only for base pairs, we call them "microstates". Let us derive a rough estimate of this folding space enlargement. The size of the folding space for a sequence of length n grows asymptotically with a · b^{ n } · n ^{3/2}, with b = 1.44358 and a = 3.45373 [8]. A structure has, on average, k(n) helices, where k grows with n. Each helix end has up to four ways to play with the dangles, but helix ends in hairpin loops do not count. Directly adjacent helices further reduce the number of dangling alternatives.
This enlargement of the search space is not a problem for MFE structure prediction. The dynamic programming algorithm derived from the grammar MicroState only does a constant amount of extra work compared to NoDangle and OverDangle. But a severe problem arises with the desire to investigate nearoptimal structures. The roughly 4^{ k } microstates of an optimal structure with k helices crowd the nearoptimal folding space, while representing the same structure in the nondangling sense. Enumerating suboptimals returns a tremendous amount of useless information. RNASUBOPT therefore uses OverDangle for enumeration, even when option d1 is specified. Afterwards, it reevaluates the energy of predicted structures using correct dangling. Hence, the ranking of structures may change. Occasionally, we observe that the energy of the true MFE structure is so much above the energy of other, overdangled structures that it falls above the energy threshold for enumeration and is not returned at all.^{7}
The second problem arises with computations that are based on Boltzmann statistics. The partition function Q sums up the Boltzmannweighted energies of all members in the folding space. Each secondary structure contributes to the partition function as many times as it has microstates, hence the result would be skewed towards structures with many microstates. The significance of this bias is hard to judge^{8}, and up to this study, it could not be evaluated empirically. For this reason, RNAFOLD does not support partition function computation with the MicroState model (option d1).
Fortunately, the partition function with correct dangles, avoiding overdangling as well as explosion of the folding space, can also be computed. To keep the folding space simple, we need a more sophisticated grammar: MacroState.
Model MacroState
The important feature of MacroState is that for any sequence, it defines the identical folding space as NoDangle. This is hard to believe when just looking at the grammar, but has been shown in [6], and is further demonstrated by the measurements shown in Figure 4. The size of the folding space, as defined by MacroState, agrees with that of NoDangle and OverDangle not only on average, but also on each individual sequence.
Extreme probability shift example
GACCAAAGCCUUUGUCCCACAAAUUGCGAUCGCGUCGCGGAGC  

MacroState prob.  MicroState prob.  shape class 
58.44%  32.58%  [][] 
29.32%  63.43%  [[][]] 
12.24%  03.99%  [] 
In this example, 40% of the probability mass is shifted by switching models, causing the order of the two topranking shapes to be reversed. To find out whether this situation is the exception or the rule is a main motivation of this study.
Results & Discussion
Data sets
The four data sets used in this study, DARTS, FR3D:3A, FR3D:4A, and RNAstrand:91 are based on RNA 3D structure data sets prepared in the context of previously published studies.
Structures drawn from PDB
We examined three datasets  DARTS, FR3D:3A, and FR3D:4A based on RNA 3D structural data sets prepared in the context of previously published studies. All three original data sets were created in order to reflect the currently available structural repertoire of RNA molecules as given by structures solved experimentally by Xray and NMR analysis.
The DARTS set was used for the analysis and classification of RNA tertiary structures in [17]. It was built from all structures available in the March 2007 version of the Protein Data Bank (PDB) [18, 19]. The DARTS data set is available at http://bioinfo3d.cs.tau.ac.il/DARTS and contains 244 structures. The creation of this data set involved dedicated structural comparisons to ensure pairwise structural and sequence variability. Unfortunately, the DARTS database is not updated anymore and therefore is limited to data deposited in the PDB before March 2007.
The two FR3D data sets [20, 21] are representative sets based on all RNA Xray structures with a resolution of up to 3 Å (246 structures containing 653 chains) and up to 4 Å (293 structures containing 764 chains), respectively, that were contained in the PDB in 2010. Both sets contain one representative structure for each group of RNA structures found similar (or identical) according to the employed sequence (> 95% identity) and structural (cf. [21]) similarity cutoffs. Both data sets FR3D:3A and FR3D:4A are available as weekly updated lists at http://rna.bgsu.edu/FR3D. The FR3D data sets were created taking recently solved structures into consideration and therefore represent the currently known RNA 3D structural space. Here, the FR3D:3A set is restricted to structures that have been solved at a better resolution and may therefore be more reliable than structures contained in the FR3D:4A set. In turn, the FR3D:4A set has a less strict resolution cutoff and therefore contains more structures.
From PDB structures to "gold" structures
In order to generate the data sets for this study, we downloaded all 3D structures contained in the original data sets from the PDB and extracted the secondary structures of each RNA chain using the stereogeometrical information encoded within the atomic coordinates. Each chain was processed with the base pair annotation software tool MCAnnotate [22] resulting in a list of all intramolecular contacts in the chain. For this study, we only used base pair interactions that are formally involved in secondary structure formation, namely the cis WatsonCrick (cWC) base pairs (G:C, C:G, A:U, U:A, G:U, U:G). All other interactions, such as noncanonical base pairs, base stackings, and basebackbone interactions were ignored since they are not part of the secondary structure. The secondary structure of an RNA chain could then be reconstructed directly from the ordered list of canonical base pairs. In a next step, this "preliminary" structure was scanned for lonely base pairs and pseudoknot interactions. Since lonely base pairs are thermodynamically unstable in a secondary structure, they were removed from the list. Due to the fact that there is no unique solution to remove the knot(s) from a pseudoknotted structure, these structures are unusable for the purpose of our study. Therefore, structures containing pseudoknots larger than one base pair, were also discarded. We consider the set of structures reduced in this way as the set of "gold" structures. They constitute our standard of truth, but we are reluctant to call them "true" structures, not only because of our removal of information, but also since structures in cristallo may be different from structures in vivo^{9}.
Our gold data sets resulting from DARTS, FR3D:3A, and FR3D:4A consist of 147, 111, and 136 structures, respectively.
As a final detail: in a few cases, FR3D:3A and FR3D:4A contain the same sequence, with different resolution in 3D and with different secondary structure derived from it. No secondary structure prediction program can be expected to be correct in both cases.
A data set derived from RNAstrand
Aside from these data sets, we also created a data set RNAstrand:91 with 91 structures from the RNAstrand database [23]. Since RNAstrand was designed as a source of validated structures, with an eye on the evaluation of RNArelated bioinformatics tools, it will be interesting to observe if the findings on this data set agree with the others.
Overall, we shall find that our four data sets deliver consistent sets of results. Therefore, the text of this article will discuss only selected measurements in detail, with the other ones given in the additional file 1, as well as all four raw data sets in additional file 2.
Evaluation of models for MFE structure prediction
While our main interest is in the effect of the chosen model on the partition function based computations, we here evaluate the four grammars with respect to prediction of a single MFE structure.
Evaluation setup
In evaluating models with respect to MFE structure prediction, we include not only our programs NoDangle and OverDangle, MicroState and MacroState, but also the folding programs UNAFOLD and RNAFOLD, which our readers are rightfully curious about because of their practical importance. Turner'99 parameters [1] were used throughout^{10}. These parameters are derived from melting experiments, with a few exceptions. Multiloop parameters such as ml _energy in Turner'99 are not derived from experiment, but are optimized from structure data to be used in conjunction with the MicroState model. Out of competition, we also include CENTROIDFOLD, which goes beyond strict energy minimization by producing a nearoptimal ensemble of structures and choosing the eventual, singlestructure prediction based on this sample.
Relative performance of programs of different origin is, however, not our main interest here. Mainly, the evaluation should support that our four grammars faithfully reproduce the behavior of the models underlying RNAFOLD with options d0, d1, and d2, as postulated at the outset of this study.
Observations from MFE prediction experiment
Consistency of implementations
Naturally, comparing the results from the same tool leads to entries of zero base pair distance in the diagonal of Figure 6. The offdiagonal zero entries, however, are quite remarkable. When two different algorithms perfectly agree in their MFE predictions on the complete data set, this provides strong evidence that they both faithfully implement the same thermodynamic model of the folding space in each of its variants. In particular, this shows that our grammars NoDangle/OverDangle and MicroState indeed capture the analysis computed by RNAFOLD with options d0/d2 and d1. The perfect zeroes might even make our reader suspicious! Occasionally, there must be two (or more) cooptimal structures of minimal free energy, and it is not formally defined which one a program should return in this situation. Hence, it is accidental whether or not two different programs, implemented by different programmers, make the same choice. We therefore have designed our new programs to report all cooptimal solutions in such a situation, and then choose the structure closest to the RNAFOLD prediction. This always delivered a perfect match.
We apply the same technique of safeguarding against cooptimals when comparing to a database structure. Note that in practice, when predicting structure for a novel RNA, the users of a structure prediction program have no reference structure to resort to. In this case, reporting all cooptimal structures makes them aware of the ambiguity of the situation, and leaves them with the choice to make. This is somewhat preferable to quietly reporting a single MFE structure, selected from several by implementation peculiarities.
The perfect agreement of MacroState with the MFE prediction of RNAFOLD d1 as well as with MicroState demonstrates that MacroState in fact computes the energy model of the other two programs, while avoiding (as explained above) their explosion of the state space. Taken together, these consistency results shows that we have correct programs set up for our second experiment, where we will evaluate the effect of the chosen energy and state space model on partition function calculations.
Quality of MFE predictions
Overall, the quality of MFE predictions compared to "real" structures is moderate when measured on the individual base pair level, with errors^{11} ranging from 16% to 21% for the gold structures. This is expected and wellknown. It is the reason why researchers have developed more advanced techniques, such as structure sampling, complete enumeration, or shape abstraction. The PDB structures contain base pairs which by definition are not predicted  nonstandard pairs, 3D interactions, pseudoknots, and lonely pairs. As explained above, the data set of gold structures has been cleaned up in these respects, and as expected, the predictions come closer, but deviations are still considerable.
The gold structures are best predicted by MacroState and MicroState (distance 521) and RNAFOLD d1 (distance 531). The small difference is accidental and arises from the rare case where RNAFOLD picks an unlucky choice from several cooptimal structures.
Performance of different dangling models
Comparing the full dangling model (MicroState, MacroState) to its upper and lower approximations NoDangle and OverDangle, we find that its proper implementation pays off. It reduces the accumulated distance by about 14% over NoDangle, and by 9% over OverDangle. Similar percentages apply for RNAFOLD option d1 versus d0 and d2. This also shows that OverDangle approximates the correct model better than NoDangle and justifies its use as a substitute for the full model in partition function calculations with RNAFOLD and RNASUBOPT, where the grammar MacroState is not available.
unafold performance
The two versions of UNAFOLD consistently score a bit worse against the gold structures than all other programs. Compared to each other, we also observe that the distance is improved by considering dangling energies, here by 17%. Otherwise, the two UNAFOLD versions cluster with the NoDangle/MicroState groups, as they should^{12}.
Looking deeper into the nearoptimal folding space
We included CENTROIDFOLD[24] as a representative of methods which, in contrast to the above programs, look deeper into the Boltzmann ensemble of nearoptimal structures. Our evaluation shows that the extra effort is well spent. CENTROIDFOLD comes closest to the good structures, and with respect to the single structure predictors, it corresponds best with the group of RNAFOLD d1, MacroState and MicroState.
Evaluating models for partition function and related computations
We will explain our evaluations in detail based on our largest data set, DARTS. Results on the other data sets are obtained in an analogous way and are summarized in the end of this section.
Evaluation Criteria
In this section, we apply probabilistic shape analysis to our data set. We are interested in the difference of performance of the four models NoDangle, OverDangle, MicroState and MacroState. For simplicity, we call the abstract shape of the reference structure the "reference shape", and refer to the most likely predicted shape as the "dominant shape", although its actual dominance within the Boltzmann ensemble will not be strong if there is another shape with similar probability. The shape string of the reference shape of sequence s is obtained by a call to RNAshapes t l D "s", where 1 is one of the five shape abstraction levels.
We ask the following questions:

What are the differences in the shape probabilities computed with each of the four models?

How is the difference affected by the shape abstraction level considered?
Since we do observe significant differences in model behavior, we also ask which model comes closer to the truth:

To what extend does the dominant shape agree with the reference shape?

What is the median (or the 75% and 90% quantile) of the reference shape among the predicted shapes?
Finally, we consider

What are the runtime or memory tradeoffs for computing with different models?
Evaluation method
Shape probabilities do not make a structure prediction per se. They provide holistic information by assigning probabilities to all shapes in the folding space of a sequence x. It is our responsibility how we interpret theses data. The hope is, of course, to find the biologically functional structure among the highprobability shapes, to find two high probability shapes for a riboswitch, to use lack of any shape with high probability as an indicator of absence of a welldefined structure, and so on. Such analysis goes beyond shape probabilities, and takes into account the concrete shreps returned for each shape.
Note that 0 ≤ SPS(x) ≤ 1, where the extreme case of 1 would only be achieved when all shapes with positive probability by grammar A have zero probability by grammar B and vice versa. The SPS can be interpreted as the overall probability mass that moves between shapes.
We chose the SPS measure because of this nice interpretation. We also evaluated two alternative measures. The squared distance of base pair probability matrices is correlated with the SPS by a factor around 0.83 at shape level 5 and not much lower on less abstract shape levels. The KullbackLeibler divergence turned out to be unsuitable for the purpose, as it is not symmetric and both versions (KL(x, y) versus KL(y, x)) show the poorest correlation among all methods tested. Details of this investigation of alternatives are given in additional file 1.
Observations
First, consider shape abstraction level 5. We find that models MacroState and MicroState show the most agreement, where the SPS is around 3.7%. MacroState shows a significant SPS against the others, strongest against NoDangle (9.6%) but also against OverDangle (5.7%). A SPS in this range means that while in many cases, the predicted dominant shape will be the same for all models, this need not hold in general.
This justifies the question which of the model finds the gold shape as the dominant shape more often (see below). By the way: the dominant shape and the shape of the MFE structure agree for MacroState in 143 out of 147 cases.
Dominant shape is gold shape?
Ratio of agreement between dominant shape and gold shape for the different grammars (columns) and different shape abstraction levels (rows).
Level  MacroState  MicroState  OverDangle  NoDangle 

5  0.823  0.816  0.796  0.810 
4  0.694  0.694  0.660  0.687 
3  0.687  0.680  0.660  0.673 
2  0.653  0.653  0.612  0.646 
1  0.585  0.551  0.565  0.592 
The best ratio of agreement of dominant shape and gold shape is 82.3%. The fact that this value is not higher is the reason which makes investigators look into several highprobability shapes and their shreps in practice. Comparing the models, we find that there is no clear winner, with a margin of only 2.7% between the best and the worst performer. (Moreover, the first position varies over our data sets.) Here, MacroState finds agreement most often, with a 0.7% margin over MicroState and 1.3% margin over NoDangle. OverDangle performs worst (79.6%), but not hopeless when we consider that one will look at a number of topranking shapes anyway.
Positions of correct shapes.
Level  MacroState  MicroState  OverDangle  NoDangle  

50%  75%  90%  100%  50%  75%  90%  100%  50%  75%  90%  100%  50%  75%  90%  100%  
5  2  2  2  8  1  2  3  12  1  2  3  10  2  2  2  4 
4  1  2  4  85  1  2  4  124  1  2  4  217  1  2  4  64 
3  1  2  4  108  1  2  6  192  1  2  5  315  1  2  5  54 
2  1  2  16  759  1  3  21  3729  1  3  13  2404  1  3  21  6534 
1  1  4  46  1373  1  4  68  6395  1  3  58  2349  1  5  42  4674 
An unexpected observation is the strong performance of shape level 2. Considering the 75% quartile, 3 shapes suffice to find the gold shape, independent of the model chosen. We will return to this observation in the Conclusion.
Relative runtime and memory consumption
Relative memory.
Level  MacroState  MicroState  OverDangle  NoDangle 

5  1.00  0.26  0.26  0.21 
4  3.90  0.76  0.76  0.53 
3  6.62  1.31  1.24  0.74 
2  139.12  6.93  7.89  7.36 
1  795.14  47.38  51.21  24.29 
Relative runtime.
Level  MacroState  MicroState  OverDangle  NoDangle 

5  1.00  0.25  0.15  0.12 
4  3.70  0.95  0.59  0.39 
3  5.99  1.59  0.96  0.60 
2  145.56  14.46  9.39  8.37 
1  643.20  117.16  51.76  28.99 
MacroState is the most sophisticated grammar and hence the most expensive to compute with. It is slower compared to MicroState, OverDangle, and NoDangle by factors of about 4.0, 6.7, and 8.3, respectively, on level 5. This slowdown factors are about the same for level 4 and 3, and increases for levels 2 and 1, but not consistently so. The largest slowdown measured is 643.20/28.99 = 22.2.
In terms of memory requirements, similar observations hold. This is clear, since all algorithms are implemented via dynamic programming, where a difference in the number of tables to be filled (with MacroState needing the most) directly maps to the difference in runtime as well as in space requirements.
Overall, the selected shape abstraction level makes more difference with resource requirements than the chosen model. For example, NoDangle (the most efficient) used with abstraction level 2 uses more time and space than MacroState (the least efficient) with abstraction levels 5, or 4.
Consistent results on data sets DARTS, FR3D:3A, FR3D:4A, and RNAstrand:91
We performed the same analysis as described above for the data set DARTS also for the data sets FR3D:3A and FR3D:4A and RNAstrand:91. Our observations on these data sets are consistent with what was reported above. Therefore, measurement results on these data sets are reported in additional file 1, but not further discussed here.
RNAstrand:91 performing similar to the PDBderived data sets demonstrates that the RNAstrand data base meets its design goal to provide a solid base of validated structures for tool evaluation [23]. Structures from RNAstrand can be selected according to specifc criteria of interest, and do not require the cleanup operations we had to perform with structures taken from PDB.
Conclusion
Model comparison
Summing up our observations from model comparison and model performance evaluation, we conclude the following:
Conclusion 1 For prediction of a single structure, there is no better alternative (among the models considered) than RNAFOLD d1, possibly augmented to report ALL structures with the optimal MFE value as in MicroState, when several exist.
However, with such augmentation, a filter must be provided to safeguard against cooptimal microstates of the same optimal macrostate being reported.
Conclusion 2 The distortion of shape probabilities caused by state space explosion (MacroState versus MicroState) is smaller than the one caused by over or underestimating energies (MacroState and MicroState versus NoDangle or OverDangle).
Models being so similar leads us to the question of runtime effort.
Conclusion 3 Since results between MacroState and MicroState differ only marginally, MicroState may be used for probability calculation. The higher computational effort of MacroState is not justified.
In the light of the previous conclusions we find:
Conclusion 4 On longer sequences, the only remaining virtue of MacroState appears to be its ability to enumerate suboptimal structures with correct energies, and without redundancy.
This answers the questions raised at the outset of this study.
Evaluation of further models
Our evaluation has concentrated on the models underlying the programs RNAFOLD, RNASHAPES, and RNASUBOPT. There are many other folding programs out there. If these implementations adhere to the abstract models we present here in the form of tree grammars, our evaluation pertains to them as well. More likely, each implementation has its own peculiarities. In fact, one may think of extending our evaluation to models that are not based on thermodynamics at all, but are derived via machine learning techniques [25, 26]. These programs could be evaluated in the setting of this study in one of two ways. Either, the program source code is extended by the computation of abstract shapes and their shape probabilities (a useful feature anyway), and applied to our data sets directly. Or, the model behind the program is extracted as a tree grammar, coded in Bellman's GAP, and combined with existing modules for shape abstraction and partition function computations. Depending on the model differences, extracting the grammar behind the code may come down to a few minor changes to the four models provided here.
Generally, the four models MacroState, MicroState, Overdangle and NoDangle are available as a starting point for future research into on thermodynamic RNA folding. Implemented in the Bellman's GAP language, these programs are especially easy to modify or extend, while the Bellman's GAP compiler provides automatic translation into efficient and correct dynamic programming algorithms. The complete source code of our four models is included in additional file 3.
A new strategy for level2 shape probabilities?
Our observations about the performance of shape level 2 gives rise to the investigation of a new strategy. Recall that level 2 gives much stronger information than levels 5 or even 3. Level 2 records not only the overall arrangement of helices, but also reports and distinguishes internal loops, 5' and 3' bulges.
Over all our data sets, consideration of (only) the five most likely level2 shapes (using MicroState) reports the gold shape in 75% of the cases, while 25 level2 shapes reach 90% coverage. However, the cost of level2 shape analysis becomes prohibitive for longer sequences. Our data show a slowdown factor of 55 (for MicroState) over level5 analysis, which should become even worse for longer sequences. Therefore, we conclude
Conclusion 5 A strategy to efficiently compute level2 shapes for long sequences is desirable
Let us sketch a strategy how this can be achieved, borrowing ideas from the RAPIDSHAPES method [27]. Directly accessing the complete level2 shape space of a long sequence appears infeasible. But we can compute a level5 analysis at 90% or 100% coverage quickly, by reporting a small number topranking level5 shapes (12 would suffice for 100% coverage on our data sets). For these shapes, we can generate a thermodynamic matcher [27] to perform a separate level2 analysis within each of the reported level5 shape classes. Generating such a matcher as a tree grammar, encoded in Bellman's GAP, plus its subsequent compilation has negligible runtime. This should reduce the computational effort (which results from the number of shapes) considerably. While this is not mathematically guaranteed to yield the most likely level2 shape, the idea appears promising.
Notes
^{1}Our observations may pertain also to other popular programs such as MFOLD[28], UNAFOLD[29] and RNASTRUCTURE[30], but their folding space implementations have not been remodeled here.
^{2}One may view our reengineering as adding shape probability functionality to the Vienna RNA package from outside.
^{3}Similarly, stacking of helices [1, 31, 32] can further contribute free energy. This aspect is not considered here.
^{4}RNAFOLDmanual: "d or d0 ignores dangling ends altogether (mostly for debugging)."
^{5}RNAFOLDmanual: "With d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the default for partition function folding (p)."
^{6}RNAFOLDmanual: "With d1 only unpaired bases can participate in at most one dangling end, this is the default for mfe folding but unsupported for the partition function folding."
^{7}A larger threshold will always help. However, one cannot tell whether this situation has occurred.
^{8}Whether or not it is adequate in partition function computations to split a secondary structure into several microstates is an unresolved dispute among experts (M. Zuker, personal communication).
^{9}This can be evaluated by experimental techniques [33], but sufficient data are not yet available.
^{10}While in press, Turner'2004 energy parameters became available. Results for all evaluations are listed in additional file 4.
^{11}It is not obvious how to convert our absolute distances into error rates. Remember that a mispredicted base pair can contribute a distance of 2 (cf. Figure 6). Assuming that predictions hold about the same number of base pairs as the gold structures (1593), the interval of possible distance scores is [0, 3186], from which the above percentages are derived.
^{12}We also looked at four further UNAFOLD variants in dangle and nodangle mode. Their behavior deviates considerably, which is explained by differences in the implemented energy model (M. Zuker, personal communication).
^{13}In theory, these tables should be symmetric. We see a small asymmetry on the last decimal position in eight cases. This results from the fact that our programs  for better speed  ignore shapes with an initial probability less that 10^{6}. This means our resulting shape lists are nor perfectly identical in the low probability tail, and together with rounding errors, this leads to discrepancies ≤ 0.002.
Declarations
Acknowledgements
Thanks go to Michael Zuker for comments on the energy model and the UNAFOLD program, and to Georg Sauthoff for support with the Bellman's GAP system. Additional thanks go to Craig Zirbel for providing the FR3D:3A data set.
We acknowledge support of the publication fee by Deutsche Forschungsgemeinschaft and the Open Access Publication Funds of Bielefeld University.
We also thank the anonymous reviewers for helpful comments on the manuscript.
Authors’ Affiliations
References
 Mathews D, Sabina J, Zuker M, Turner D: Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288: 911–940. 10.1006/jmbi.1999.2700View ArticlePubMedGoogle Scholar
 Hofacker IL, Fontana W, Stadler PF, Bonhoeffer SL, Tacker M, Schuster P: Fast Folding and Comparison of RNA Secondary Structures. Monatsh Chem 1994, 125: 167–188. 10.1007/BF00818163View ArticleGoogle Scholar
 Giegerich R, Voß B, Rehmsmeier M: Abstract shapes of RNA. Nucleic Acids Research 2004, 32(16):4843. 10.1093/nar/gkh779PubMed CentralView ArticlePubMedGoogle Scholar
 Wuchty S, Fontana W, Hofacker IL, Schuster P: Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 1999, 49(2):145–165. 10.1002/(SICI)10970282(199902)49:2<145::AIDBIP4>3.0.CO;2GView ArticlePubMedGoogle Scholar
 Dowell R, Eddy S: Evaluation of several lightweight stochastic contextfree grammars for RNA secondary structure prediction. BMC Bioinformatics 2004, 5: 71. [http://www.biomedcentral.com/1471–2105/5/71] 10.1186/14712105571PubMed CentralView ArticlePubMedGoogle Scholar
 Voß B, Giegerich R, Rehmsmeier M: Complete probabilistic analysis of RNA shapes. BMC Biology 2006, 4: 5. 10.1186/1741700745PubMed CentralView ArticlePubMedGoogle Scholar
 Waterman M: Introduction to computational biology. Maps, sequences and genomes. London: Chapman & Hall; 1995.View ArticleGoogle Scholar
 Nebel M, Scheid A: On quantitative effects of RNA shape abstraction. Theory in Biosciences 2009, 128: 211–225. [10.1007/s12064–009–0074z] [10.1007/s120640090074z] 10.1007/s120640090074zView ArticlePubMedGoogle Scholar
 Janssen S, Reeder J, Giegerich R: Shape based indexing for faster search of RNA family databases. BMC Bioinformatics 2008, 9: 131+. 10.1186/147121059131PubMed CentralView ArticlePubMedGoogle Scholar
 Borer P, Dengler B, Tinoco I Jr, Uhlenbeck O: Stability of ribonucleic acid doublestranded helices. J Mol Biol 1974, 86: 843–853. 10.1016/00222836(74)90357XView ArticlePubMedGoogle Scholar
 Burkard M, Kierzek R, Turner D: Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. J Mol Biol 1999, 290: 967–982. 10.1006/jmbi.1999.2906View ArticlePubMedGoogle Scholar
 Ohmichi T, Nakano S, Miyoshi D, Sugimoto N: Long RNA dangling end has large energetic contribution to duplex stability. J Am Chem Soc 2002, 124: 10367–10372. 10.1021/ja0255406View ArticlePubMedGoogle Scholar
 Liu J, Zhao L, Xia T: The dynamic structural basis of differential enhancement of conformational stability by 5' and 3'dangling ends in RNA. Biochemistry 2008, 47: 5962–5975. 10.1021/bi800210tView ArticlePubMedGoogle Scholar
 Giegerich R, Meyer C, Steffen P: A discipline of dynamic programming over sequence data. Science of Computer Programming 2004, 51(3):215–263. 10.1016/j.scico.2003.12.005View ArticleGoogle Scholar
 Giegerich R, Sautho G: Yield grammar analysis in the Bellman's GAP compiler. In Proceedings of the Eleventh Workshop on Language Descriptions, Tools and Applications. LDTA 2011, ACM; 2011.Google Scholar
 Sauthoff G, Janssen S, Giegerich R: Bellman's GAP  A Declarative Language for Dynamic Programming. 13th International ACM SIGPLAN Symposium on Principles and Practice of Declarative Programming, PPDP 2011. ACM 2011 ACM 2011Google Scholar
 Abraham M, Dror O, Nussinov R, Wolfson H: Analysis and classification of RNA tertiary structures. RNA 2008, 14(11):2274. 10.1261/rna.853208PubMed CentralView ArticlePubMedGoogle Scholar
 Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P: The protein data bank. Nucleic Acids Res 2000, 28: 235–242. 10.1093/nar/28.1.235PubMed CentralView ArticlePubMedGoogle Scholar
 Rose P, Beran B, Bi C, Bluhm W, Dimitropoulos D, Goodsell D, Prlic A, Quesada M, Quinn G, Westbrook J, Young J, Yukich B, Zardecki C, Berman H, Bourne P: The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res 2010, 39: D392–401.PubMed CentralView ArticlePubMedGoogle Scholar
 Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB: FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol 2008, 56(1–2):215–252.PubMed CentralView ArticlePubMedGoogle Scholar
 Stombaugh J, Zirbel CL, Westhof E, Leontis NB: Frequency and isostericity of RNA base pairs. Nucleic Acids Res 2009, 37(7):2294–2312. 10.1093/nar/gkp011PubMed CentralView ArticlePubMedGoogle Scholar
 Gendron P, Lemieux S, Major F: Quantitative analysis of nucleic acid threedimensional structures. J Mol Biol 2001, 308(5):919–936. 10.1006/jmbi.2001.4626View ArticlePubMedGoogle Scholar
 Andronescu M, Bereg V, Hoos H, Condon A: RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinformatics 2008, 9: 340. 10.1186/147121059340PubMed CentralView ArticlePubMedGoogle Scholar
 Hamada M, Kiryu H, Sato K, Mituyama T, Asai K: Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 2009, 25(4):465–473. 10.1093/bioinformatics/btn601View ArticlePubMedGoogle Scholar
 Do CB, Woods DA, Batzoglou S: CONTRAfold: RNA secondary structure prediction without physicsbased models. Bioinformatics 2006, 22(14):e90–98. 10.1093/bioinformatics/btl246View ArticlePubMedGoogle Scholar
 Andronescu M, Condon A, Hoos H, Mathews DH, Murphy KP: Computational approaches for RNA energy parameter estimation. RNA 2010, 16(12):2304–2318. 10.1261/rna.1950510PubMed CentralView ArticlePubMedGoogle Scholar
 Janssen S, Giegerich R: Faster computation of exact RNA shape probabilities. Bioinformatics 2010, 26(5):632–639. 10.1093/bioinformatics/btq014PubMed CentralView ArticlePubMedGoogle Scholar
 Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31: 3406–3415. 10.1093/nar/gkg595PubMed CentralView ArticlePubMedGoogle Scholar
 Markham NR, Zuker M: UNAFold: software for nucleic acid folding and hybridization. Methods in molecular biology (Clifton, N.J.) 2008, 453: 3–31. 10.1007/9781603274296_1View ArticleGoogle Scholar
 Reuter J, Mathews D: RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 2010, 11: 129. 10.1186/1471210511129PubMed CentralView ArticlePubMedGoogle Scholar
 Walter A, Turner D, Kim J, Lyttle M, Müller P, Mathews D, Zuker M: Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Nat Acad Sci USA 1994, 91: 9218–9222. 10.1073/pnas.91.20.9218PubMed CentralView ArticlePubMedGoogle Scholar
 Xia T, SantaLucia J, Burkard M, Kierzek R, Schroeder S, Jiao X, Cox C, Turner D: Thermodynamic parameters for an expanded nearestneighbor model for formation of RNA duplexes with WatsonCrick base pairs. Biochemistry 1998, 37: 14719–14735. 10.1021/bi9809425View ArticlePubMedGoogle Scholar
 Gherghe C, Shajani Z, Wilkinson K, Varani G, Weeks K: Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA. J Am Chem Soc 2008, 130(37):12244–5. 10.1021/ja804541sPubMed CentralView ArticlePubMedGoogle Scholar
 Gardner P, Giegerich R: A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 2004, 5: 140. 10.1186/147121055140PubMed CentralView ArticlePubMedGoogle Scholar
Copyright
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.