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This study presents a strategy for reducing the effects of noise on the location of RNA motifs in the context of a previously developed analysis pipeline. The pipeline was developed to search for novel RNA motifs incorporating both primary and secondary structure. The ability of the pipeline to detect motifs in the presence of a relatively large amount of sequence not containing a target motif is...
In solving the question of alignment of two RNA secondary structures, it is not clear how to choose parameters for the introduction of gaps in the alignment. We introduce a Bayesian approach for aligning two RNA secondary structures. The algorithm can not only compute the optimal alignment itself but also some interesting posteriors such as posteriors of substitution matrix and gap opening penalties...
This paper explores the use of the fuzzy C-means clustering algorithm for inferring functional relationships among proteins from their phylogenetic profiles. We conducted a series of experiments using phylogenetic profiles provided by the Cluster of Orthologous Groups of Proteins (COG) database. Experimental results demonstrate that the increasing expressiveness of fuzzy C-means enables the discovery...
Random environment of the cell demands for a stochastic tool to analyze its behavior and bring the aspects of the bio-process that has been shadowed by the kinetic rate law based approach. In this work we present a novel random walk approach to detect the dynamics of passive diffusion of a metabolite in the gram-negative bacteria through phosphoenolpyruvate phospho-transfer system (pts pathway). We...
Sequencing technologies used to generate long strands of DNA are susceptible to laboratory errors that may result in several DNA nucleotides being deleted from the genome. Detecting such deletions in the protein coding regions is of utmost importance. Missing even a single nucleotide may lead to frame shifts with all the following codons (and consequently the encoded amino acids) being identified...
Quantum mechanics and molecular dynamic simulation provide important insights into structural configurations and molecular interaction data today. To extend this atomic/molecular level capability to system level understanding, we propose an "in silico" stochastic event based simulation technique. This simulation characterizes the time domain events as random variables represented by probabilities...
The following topics are dealt with: protein-protein interaction; cancer informatics; disease informatics; protein folding; gene networks; biosequence analysis; biochemical modeling; microarray analysis; biological theory; medical informatics; RNA structure; and RNA function
Ribonucleic acid (RNA) plays fundamental roles in cellular processes and its structure is directly related to its functions. This paper describes and presents a novel algorithm for RNA secondary structure prediction based on simulated annealing (SA). SA is known to be effective in solving many different types of minimization problems and for finding the global minima in the solution space. Based on...
Complex clinical phenotypes arise from the concerted interactions among the myriad components of a biological system. Therefore, comprehensive models can only be developed through the integrated study of multiple types of experimental data gathered from the system in question. The Random Foreststrade(RF) method is adept at identifying relevant features having only slight main effects in high-dimensional...
Two extensive analyzes on RnaPredict, an evolutionary algorithm for RNA folding, are presented here. The first study evaluates the performance of individual nearest neighbor (INN) and individual nearest neighbor-hydrogen bond (INN-HB), two stacking-energy thermodynamic models; the criteria for comparison is the correlation between the prediction accuracy and the free energy of predicted structures...
Scleroderma is an autoimmune disease of the connective tissues, which thickens and hardens the affected areas. Recently, researchers have found evidence that genes are important factors for this disease, and there exist consistent differences in the patterns of gene expressions of skin biopsies from affected and non-affected individuals. In this paper, we apply genetic programming (GP) on the gene...
This work presents differential evolution (DE), applied to the problem of protein folding, using the hydrophobic-polar model. Protein folding is a relevant problem in bioinformatics for which many heuristic algorithms have been proposed. DE is a relatively recent evolutionary algorithm, and has been used successfully to several engineering optimization problems, usually with continuous variables....
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