Multiple Sequence alignment using Genetic Algorithm project (MSA) is a tool for extracting the relationship between lots of sequences. It aligns each sequence, such that one base in a sequence corresponds to bases in other sequences to reveal the similarity of genetic gene. Multiple Sequence Alignment problem is related to Artificial Intelligence, Bio Informatics and it comes under NP_ complete problem. There are no classical algorithms for solving NP_ complete problems. So we go for approximation methods. Genetic Algorithm (GA) have been proven to be robust, flexible and efficient in vast complex spaces including NP_ complete problems. The genetic algorithm is used in the sciences, engineering and the business world. This algorithm has now been successfully applied to optimization problems, scheduling, data fitting, clustering trend spotting and path finding.
Multiple Sequence alignment using Genetic Algorithm MODULES – PURPOSE AND DESCRIPTION
This section contains the basic modules in the design.
Genetic Algorithm Module
This module is used to find multiple sequence alignment using genetic algorithm. The basic or most important operators in this module are selection or reproduction, crossover and mutation. In this module first take the initial population that contain the given initial sequences. Then reproduce the initial population by inserting gaps between them and then apply crossover and mutation operators on those sequences. This process is to be continued until we get the optimal or most appropriate solution.
The various steps involved in this module are represented by the figure shown below.
USER INTERFACE MODULE:
The class sagui contains several methods for designing an easy and user friendly MSA application. It gets the input a set of sequences that are to be aligned and also parameters used for running genetic algorithm. The input sequences are appended to the text area provided by the user. The parameters are Generations, Populations , gaps, %crossover, %Mutation. This module is implemented by using the java package SWINGS. This package provided the user friendly window.
After aligning the sequences the result is appended to this textarea . the result contains the score o f the alignment and how much time required for aligning those sequences.