Plenary Lecture
Visualization of the DNA Sequences Using Self Organizing Maps
Associate Professor Hiroshi Dozono
Saga University
E-mail: hiro@dna.ec.saga-u.ac.jp
Abstract: Next generation sequencing (NGS) has recently produced large amounts of sequencing data that require more efficient methods for assembly and analysis. The produced sequences have applications in many areas of genomic science. Metagenome analysis and comparative genome analysis are examples of such applications. Metagenome analysis uses a mixture of genomes from multiple species, and the composition of species-specific sequences or expressed sequences is analyzed. Comparative genome analysis, on the other hand, infers evolutional relations and species diversity. For both applications, a global comparison of DNA sequences among species is required.
For a global comparison of DNA sequences, a Self-Organizing Map (SOM) is often used. SOM is an artificially constructed neural network. SOMs use the architecture of feed forward networks and are trained by unsupervised learning. A set of input vectors is provided, vector similarity is analyzed, and the SOM maps the input vectors on a 2-dimensional plane.
We have developed SOM algorithms which based on the N-tuples of DNA probes, frequency of the N-tuples, context of DNA sequences, Hidden Markov Model(HMM) of DNA sequences and correlation coefficients of nucleotides. In this speech, the algorithm of SOM for the analysis of DNA sequences, and the results of the analysis will be presented.
Brief Biography of the Speaker: Hiroshi Dozono graduated from Kyoto University, Japan in 1984, and graduated Doctor cource of Kyoto Univeristy in 1989. He worked in Tokushima University for two years, and in Kumamoto University for three years and currently works in Saga University as Associate Professor. His research area is Object Oriented System, Knowledge Engineering, Control Theory, Artificial Intelligence, Evolutional Algotithm Neural Networks. Recently, he specialized in application of Self Organizing Maps to Bioinformatics, Security Systems, and Control systems. He is author of about 50 papers published in international journals and conference proceedings.