RESUMO
Understanding the numerous functions of RNAs depends critically on the knowledge of their three-dimensional (3D) structure. In contrast to the protein field, a much smaller number of RNA 3D structures have been assessed using X-ray crystallography, NMR spectroscopy, and cryomicroscopy. This has led to a great demand to obtain the RNA 3D structures using prediction methods. The 3D structure prediction, especially of large RNAs, still remains a significant challenge and there is still a great demand for high-resolution structure prediction methods. In this chapter, we describe RNAComposer, a method and server for the automated prediction of RNA 3D structures based on the knowledge of secondary structure. Its applications are supported by other automated servers: RNA FRABASE and RNApdbee, developed to search and analyze secondary and 3D structures. Another method, RNAlyzer, offers new way to analyze and visualize quality of RNA 3D models. Scope and limitations of RNAComposer in application for an automated prediction of riboswitches' 3D structure will be presented and discussed. Analysis of the cyclic di-GMP-II riboswitch from Clostridium acetobutylicum (PDB ID 3Q3Z) as an example allows for 3D structure prediction of related riboswitches from Clostridium difficile 4, Bacillus halodurans 1, and Thermus aquaticus Y5.1 of yet unknown structures.
Assuntos
Modelos Moleculares , RNA Bacteriano/química , Riboswitch , Software , Sequência de Bases , Clostridioides difficile/genética , Clostridium acetobutylicum/genética , GMP Cíclico/análogos & derivados , GMP Cíclico/metabolismo , Internet , Dados de Sequência Molecular , Conformação de Ácido Nucleico , RNA/químicaRESUMO
An algorithm is proposed to provide the tool for an automatic resonance assignment of 2D-NOESY spectra of RNA duplexes. The algorithm, based on a certain subproblem of the Hamiltonian path, reduces a number of possible connections between resonances within aromatic and anomeric region of 2D-NOESY spectra. Appropriate pathways between H6/H8 and H1' resonances were obtained by subsequent implementation of experimental data as limiting factors. Predictive power of the algorithm was tested on both experimental and simulated data for RNA and DNA duplexes.
Assuntos
Algoritmos , Ressonância Magnética Nuclear Biomolecular , Ácidos Nucleicos Heteroduplexes/química , Oligodesoxirribonucleotídeos/química , Oligorribonucleotídeos/química , Software , Simulação por Computador , Conformação de Ácido NucleicoRESUMO
MOTIVATION: A formulation of a new problem of the restriction map construction based on a simplified digestion experiment and a development of an algorithm for solving both ideal and noisy data cases of the introduced problem. RESULTS: A simplified partial digest problem and a branch and cut algorithm for finding the solution of the problem.
Assuntos
DNA/genética , Mapeamento por Restrição/estatística & dados numéricos , Algoritmos , Biologia Computacional , Interpretação Estatística de DadosRESUMO
The problem addressed in this paper is concerned with DNA sequencing by hybridization. An algorithm is proposed that solves a computational phase of this approach in the presence of both positive and negative errors resulting from the hybridization experiment. No a priori knowledge of the nature and source of these errors is required. An extensive set of computational experiments showed that the algorithm behaves surprisingly well if only positive errors appear. The general case, where positive and negative errors occur, can be also solved satisfactorily for an error rate up to 10%.
Assuntos
Algoritmos , Sequência de Bases , DNA/química , DNA/genética , Biologia Computacional/métodos , Modelos Estatísticos , Reprodutibilidade dos TestesRESUMO
MOTIVATION: Reconstruction of the original DNA sequence in the sequencing by the hybridization approach (SBH) requires computational support due to a large number of possible combinations. One can notice a lack of algorithms admitting false-negative data and giving in addition all possible solutions. RESULTS: In this paper, a new method of sequencing has been proposed. An algorithm based on its idea (for the general case, when some data are missing, like in the real experiment) has been implemented and tested. Authentic DNA sequences have been used for testing. A parallel version of the algorithm has also been implemented and tested. The quality of the reconstruction is satisfactory for the library of oligonucleotides of length between 8 and 12, and 100, 200 and 300 bp long sequences. A way to a further decrease in the computation time is also suggested.
Assuntos
Algoritmos , Análise de Sequência de DNA/métodos , Sequência de Bases , DNA/genética , Estudos de Avaliação como Assunto , Reações Falso-Negativas , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Análise de Sequência de DNA/estatística & dados numéricosRESUMO
The paper is concerned with a computational phase of the sequencing DNA chains by hybridization. It is assumed that positive faults can occur in the hybridization experiment. An approach based on a reduction of the problem to a variant of a Selective Traveling Salesman Problem and an algorithm for solving the latter, have been proposed. The algorithm behaves extremely well, even for a fault rate exceeding 50%.
