# Multiple Sequence alignment using Genetic Algorithm Project

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.