Design And Implementation Of Gene Mutation Simulator

With the development of science and technology and medical treatment,according to the gene mutation features, more and more medical workers begin to doresearch on the drugs which will match the patients’ biological characteristics better,in order to replace those general medicines. Such research will require a largenumber of gene mutation data, and such data need the assistance of software.This thesis is on the basis of the project GmSim (Gene Mutation Simulator),and is the software simulation and computerization for the gene mutation progress.According to the requirement of medical workers, GmSim will do the geneticmutations with different types, positions and operations on a group of originalchromosome. Meanwhile, GmSim will produce the data with different format tosimulate the DNA sequencing data. GmSim will finally give users a group ofexpected mutation information and results, to help those projects that take charge ofthe relation between mutations and disease.This thesis, based on the biological formula and conception, uses the UNIXstandard C programming as the coding language and Linux as the researchenvironment, and makes the chromosome bases as operation units. GmSim willparse the biological and medical files, and do different types of mutations accordingto the data recorded in these files. The mutations will be classified into two kinds,i.e. automatic mutations and manual mutations. Automatic mutations will make themutations occur based on the probability and formula, while manual mutations willmake the mutations happen based on the requirement of users. There are severaltypes of mutations, including single nucleotide polymorphism, substitution,insertion, and deletion mutation, etc. After the operations of mutation, GmSim willcut the chromosome into fragments called reads, which will be organized into datawith proper format in order to simulate the DNA sequencing data. The thesis usesthe idea of software engineering to create a software model for the problem, anddevelopes GmSim after requirement specification, design, implementation andtesting. GmSim uses the technology of thread pool and the pipeline structure as theparallelization and acceleration to increase the operation efficiency.Through the research of this thesis and the design, implementation and test ofthe project, GmSim finally can analyze the different kinds of genetic files, and makethe different types of mutations based the input chromosome, and export theappropriate process and results’ description, and archieve the goal of the project.