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1.
A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure. All admissible solutions belong to the configuration space and can be obtained directly from its basis.  相似文献   

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The RNA secondary structure prediction is a classical problem in bioinformatics. The most efficient approach to this problem is based on the idea of a comparative analysis. In this approach the algorithms utilize multiple alignment of the RNA sequences and find common RNA structure. This paper describes a new algorithm for this task. This algorithm does not require predefined multiple alignment. The main idea of the algorithm is based on MEME-like iterative searching of abstract profile on different levels. On the first level the algorithm searches the common blocks in the RNA sequences and creates chain of this blocks. On the next step the algorithm refines the chain of common blocks. On the last stage the algorithm searches sets of common helices that have consistent locations relative to common blocks. The algorithm was tested on sets of tRNA with a subset of junk sequences and on RFN riboswitches. The algorithm is implemented as a web server (http://bioinf.fbb.msu.ru/RNAAlign/).  相似文献   

4.
In general RNA prediction problem includes genetic mapping, physical mapping and structure prediction. The ultimate goal of structure prediction is to obtain the three dimensional structure of bimolecules through computation. The key concept for solving the above mentioned problem is the appropriate representation of the biological structures. Even though, the problems that concern representations of certain biological structures like secondary structures either are characterized as NP-complete or with high complexity, few approximation algorithms and techniques had been constructed, mainly with polynomial complexity, concerning the prediction of RNA secondary structures. In this paper, a new class of Motzkin paths is introduced, the so-called semi-elevated inverse Motzkin peakless paths for the representation of two interacting RNA molecules. The basic combinatorial interpretations on single RNA secondary structures are extended via these new Motzkin paths on two RNA molecules and can be applied to the prediction methods of joint structures formed by interacting RNAs.  相似文献   

5.
The morphogenetic events that give rise to a specific body pattern have to date avoided extensive elucidation. Extant models of pattern formation have dealt almost exclusively with the "primary patterning" of structures in the embryo. These "universal" models fail to explain many morphological conditions, such as the simultaneous change in position of the limbs, celom, mesonephros, and umbilical artery relative to the somites as a result of a single mutation. In the present paper, we propose that the relation between two non-periodic waves may function to determine the position of "secondary structures", such as the limbs, in the embryo, relative to primary structures such as the somites. We propose that if two morphogenetic events are initiated at different times from the same region of the embryo, and are progressing in a cranio-caudal sequence at different rates, then the location of a given structure along the body axis can be described as a function of the two events. Applications and predictions based on the proposal are presented. Evidence from observations of morphogenetic events in the chick embryo, which tend to support the model, are also presented.  相似文献   

6.

Background  

Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures.  相似文献   

7.
We suggest a new algorithm to search a given set of the RNA sequences for conserved secondary structures. The algorithm is based on alignment of the sequences for potential helical strands. This procedure can be used to search for new structured RNAs and new regulatory elements. It is efficient for the genome-scale analysis. The results of various tests run with this algorithm are shown.  相似文献   

8.
We present an algorithm for prediction of RNA secondary structures.The program consists of three parts: the first computes locationand free energy of every possible stem–loop structure,the second computes probability of its formation, and the thirdlists the positions and free energies of all the stem–loopsin the order of their probability sizes. The circular RNA moleculeof chrysanthemum stunt viroid was used as an input data fordemonstrating the operation of the program. Received on March 14, 1985; accepted on March 18, 1985  相似文献   

9.
A statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences. Four nucleotide alphabets are used: two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet. RNA secondary structures are made of structural elements, such as stacks, loops, joints, and free ends. Statistical properties of these elements are computed for small RNA molecules of chain lengths up to 100. The results of RNA structure statistics depend strongly on the particular alphabet chosen. The statistical reference is compared with the data derived from natural RNA molecules with similar base frequencies. Secondary structures are represented as trees. Tree editing provides a quantitative measure for the distance dt, between two structures. We compute a structure density surface as the conditional probability of two structures having distance t given that their sequences have distance h. This surface indicates that the vast majority of possible minimum free energy secondary structures occur within a fairly small neighborhood of any typical (random) sequence. Correlation lengths for secondary structures in their tree representations are computed from probability densities. They are appropriate measures for the complexity of the sequence-structure relation. The correlation length also provides a quantitative estimate for the mean sensitivity of structures to point mutations. © 1993 John Wiley & Sons, Inc.  相似文献   

10.
Dynamic programming algorithms that predict RNA secondary structure by minimizing the free energy have had one important limitation. They were able to predict only one optimal structure. Given the uncertainties of the thermodynamic data and the effects of proteins and other environmental factors on structure, the optimal structure predicted by these methods may not have biological significance. We present a dynamic programming algorithm that can determine optimal and suboptimal secondary structures for an RNA. The power and utility of the method is demonstrated in the folding of the intervening sequence of the rRNA of Tetrahymena. By first identifying the major secondary structures corresponding to the lowest free energy minima, a secondary structure of possible biological significance is derived.  相似文献   

11.

Background  

Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases.  相似文献   

12.
An algorithm for comparing multiple RNA secondary structures   总被引:1,自引:0,他引:1  
A new distributed computational procedure is presented for rapidlydetermining the similarity of multiple conformations of RNAsecondary structures. A data abstraction scheme is utilizedto reduce the quantity of data that must be handled to determinethe degree of similarity among multiple structures. The methodhas been used to compare 200 structures with easy visualizationof both those structures and substructures that are similarand those that are vastly different. It has the capability ofprocessing many more conformations as a function of researchrequirements. The algorithm is described as well as some suggestionsfor future uses and extensions. Received on October 29, 1987; accepted on May 4, 1988  相似文献   

13.
In this paper, we proposed a 3-D graphical representation of RNA secondary structures. Based on this representation, we outline an approach by constructing a 3-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with RNA secondary structure. The examination of similarities/dissimilarities among the secondary structure at the 3'-terminus of different viruses illustrates the utility of the approach.  相似文献   

14.
Many different programs have been developed for the prediction of the secondary structure of an RNA sequence. Some of these programs generate an ensemble of structures, all of which have free energy close to that of the optimal structure, making it important to be able to quantify how similar these different structures are. To deal with this problem, we define a new class of metrics, the mountain metrics, on the set of RNA secondary structures of a fixed length. We compare properties of these metrics with other well known metrics on RNA secondary structures. We also study some global and local properties of these metrics.  相似文献   

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RNA secondary structures and their prediction   总被引:1,自引:0,他引:1  
This is a review of past and present attempts to predict the secondary structure of ribonucleic acids (RNAs) through mathematical and computer methods. Related areas covering classification, enumeration and graphical representations of structures are also covered. Various general prediction techniques are discussed, especially the use of thermodynamic criteria to construct an optimal structure. The emphasis in this approach is on the use of dynamic programming algorithms to minimize free energy. One such algorithm is introduced which comprises existing ones as special cases. Issued as NRCC No. 23684.  相似文献   

18.
BACKGROUND: A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward approach is to compute circular structures from 'internal' and 'external' substructures separated by a base pair. This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only. RESULT: Here we describe how circular secondary structures can be obtained without additional memory requirements as a kind of 'post-processing' of the linear structures. AVAILABILITY: The circular folding algorithm is implemented in the current version of the of RNAfold program of the Vienna RNA Package, which can be downloaded from http://www.tbi.univie.ac.at/RNA/  相似文献   

19.
We here present a dynamic programming algorithm which is capable of calculating arbitrary moments of the Boltzmann distribution for RNA secondary structures. We have implemented the algorithm in a program called RNA-VARIANCE and investigate the difference between the Boltzmann distribution of biological and random RNA sequences. We find that the minimum free energy structure of biological sequences has a higher probability in the Boltzmann distribution than random sequences. Moreover, we show that the free energies of biological sequences have a smaller variance than random sequences and that the minimum free energy of biological sequences is closer to the expected free energy of the rest of the structures than that of random sequences. These results suggest that biologically functional RNA sequences not only require a thermodynamically stable minimum free energy structure, but also an ensemble of structures whose free energies are close to the minimum free energy.  相似文献   

20.
Within this paper we investigate the Bernoulli model for random secondary structures of ribonucleic acid (RNA) molecules. Assuming that two random bases can form a hydrogen bond with probability p we prove asymptotic equivalents for the averaged number of hairpins and bulges, the averaged loop length, the expected order, the expected number of secondary structures of size n and order k and further parameters all depending on p. In this way we get an insight into the change of shape of a random structure during the process . Afterwards we compare the computed parameters for random structures in the Bernoulli model to the corresponding quantities for real existing secondary structures of large subunit rRNA molecules found in the database of Wuyts et al. That is how it becomes possible to identify those parameters which behave (almost) randomly and those which do not and thus should be considered as interesting, e.g., with respect to the biological functions or the algorithmic prediction of RNA secondary structures.  相似文献   

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