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It is important to identify DNA motifs in promoter regions to understand the mechanism of gene regulation. Computational approaches for finding DNA motifs are well recognized as useful tools to biologists, which greatly help in saving experimental time and cost in wet laboratories. Self-organizing maps (SOMs), as a powerful clustering tool, have demonstrated good potential for problem solving. However,...
Analysis of DNA sequences requires conversion of a base sequence to a numerical sequence. The choice of the numerical mapping of a DNA sequence affects how well its biological properties can be reflected in the numerical domain for the detection of regions of interest. This paper presents twelve one-sequence numerical representation methods and a discrete Fourier transform (DFT) based approach to...
An optimized numerical mapping scheme for achieving improved location of exons in DNA sequences using digital filters is proposed. Characteristic numerical values for the four nucleotides, referred to as pseudo-EIIP values, are obtained using a training procedure where the location accuracy is maximized using a quasi-Newton algorithm based on the Broyden-Fletcher-Goldfarb-Shanno updating formula....
Classification of organisms into different categories using their genomic sequences has found importance in study of evolutionary characteristics, specific identification of previously unknown organisms, study of mutual relationships between organisms and many other aspects in the study of living things. Chaos game representation (CGR) uniquely represents DNA sequences and reveals hidden patterns...
Support vector machines (SVMs) are known to be excellent algorithms for classification problems. The principal disadvantage of SVMs is due to its excessive training time in large data set, such as DNA sequences. This paper presents a novel SVMs classification method which reduces significantly the input data set using Bayesian technique. Using this system, we are able to predict with a high accuracy...
Due to the enormous amount of DNA sequences to be processed, the computational speed is an important issue to be considered. Although relatively high accuracy has been achieved by existing methods, most of these prediction methods are computationally intensive. In this paper, a novel method for predicting DNA splice sites using improved bayesian classifier is presented. Naive bayesian classifier is...
Polymerase chain reaction (PCR), though invented over twenty years ago and having been developed with much advance, still face challenges nowadays. Long DNA and most high GC content DNA sequences are still hard to amplify. People have had few tools to predict whether a PCR is successful or not before a real PCR experiment is done. In this study, 189 randomly selected short amplicons from human genome...
Classification is a major task in the gene sequence analysis. Based on the general principle of artificial immune system, this paper first constructed a classifier which inducted antibody-antigen identification, immune colonel reproduction, hypermutation, affinity mature and the network suppression, by simulating how the antigens stimulate the immune network and how the immune network responds. Then,...
The model species genomes project has played a very important role in the research of human genomes. By comparing and identifying the genomes' information in the different biological evolution stages with the model species genomes, it is favorable to understand deeply the genomes' structure and function of the advanced species, especially the human being, and to reveal the life's essential law. In...
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