(99) DNA Sequence Analysis using Hidden Markov Model and Genetic Algorithm

	Machine:     UNIX Machine
	Environment: UNIX
	Language:    C
	Source Code: 250 KB
	Documents:   User's Manual (English / Japanese)

Overview

This program extracts signal patterns in DNA sequences using Hidden Markov Model (HMM) and Genetic Algorithm (GA).

Features

Extraction of signal patterns is one of important problems in genetic information processing. The patterns are utilized for considering DNA-protein interaction and predicting functional sites in gene identification. This program extracts signal patterns in DNA sequences using HMM and GA. The patterns are expressed in the form of HMM. The topology of HMM is optimized by GA evaluating the likelihood of HMM and complexity of the topology. A subroutine for evaluating each HMM is impremented as a process, and executed concurrently.

Function

  1. Expressing signal patterns in the form of HMM.
  2. Optimizing the topology of HMM by GA evaluating the likelihood of HMM and complexity of the topology.
  3. Evaluating each HMM in parallel.
  4. Predicting functional sites and discriminating DNA sequences using an obtained HMM.

FTP

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