Design And Implementationon Single Nucleotide Polymorphisms Identification Software

In recent years,the rapid development of next-generation sequencing technology accelerated the study of genes.The completion of the 1000 Genomes Project also marks that the mankind entered the post-genome era,scientists main study the effect of genome sequence of individual characteristicsin the post-genome era.Single Nucleotide Polymorphism(SNP)as one of the important genetic markers,has been widely concerned in the research of SNP in the genome sequences.More and more methods are applied to the detecting of SNP.However,most of the methods of SNP detection are expensive,and the speed is slow and it is difficult to accurately locate the SNP site in the massive SNP brush.Therefore,this paper studies how to identify the SNP site information more quickly and accurately in the genome sequence.This article is based on the second generation sequencing technology,in view of the problems identify SNP site in the genome sequence,in order to realize accurate position and quickly find the SNP site,the research group designand optimize the software of identifying SNP.The software design based on the logic regression model and the Bayesian framework mainly consists of three modules which aredata preprocessing,gene mapping,SNP identification.Data preprocessing module mainly completes data acquisition and data transformation;Gene mapping module mapped NGS data to the reference sequence,and the SNP information of base substitutuins was obtained;SNP recognition module is mainly to complete the detection of real SNP.In the end of this paper,the Torque-PBS cluster management system is used to detect the SNP site of the optimized software and the original software to obtain the time of detecting the site and compared it.Experiments show that designing and optimized SNP detection method is not only on the testing time was shortened obviously(the test of time just before the method of 1/3-1/2),but also made full use of computing resources.