Research And Software Development Of Tetraploid Haplotype Reconstruction Algorithm

Gene polymorphism from single nucleotide polymorphism(Single Nucleotide Polymorphisms,SNP),analysis and research has important significance in the field of biological genetics SNP.Composed of the sequences of the SNP loci haplotype,carrying more genetic information than single SNP.Haplotype analysis and detection for understanding gene function,the diagnosis of complex diseases and accurate positioning genetic gene plays an important role.Unfortunately,the current use of biological methods for direct determination of haplotype costs too expensive.So,the use of computer technology to identify and reconstruct the haplotype,has great practical significance.This research focuses on the past with the diploid,the research level of further development and adapt to the needs of social development have studied the reconstruction problem more times body.This paper mainly focuses on the study of tetraploid and tetraploid for haplotype reconstruction problem is proposed based on MEC/GI model(the Minimum Error Correction with Genotype Information,with genotype minimum error correction model)EHTS algorithm and EHTD algorithm.The EHTS algorithm calculates the support of all permutations of each haplotype of the haplotype,and selects the largest rank of the support value as the SNP value of the site.This process is repeated iteratively until all loci are determined and the haplotype is determined.Through the algorithm contrast experiment,EHTS algorithm has good performance under various parameters,runs faster and has higher reconstruction rate than W-GA and Q-PSO algorithm.The EHTD algorithm mainly calculates the difference degree of each locus,and selects the smallest permutation of the dissimilarity degree to reconstruct the haplotype.Experimental results show that the proposed algorithm has better reconstruction performance than W-GA and Q-PSO algorithm.In a few cases,EHTD has a higher rate of reconstruction than the EHTS algorithm.Based on the EHTD and EHTS algorithm on the basis of the experiment,to design a tetraploid haplotype reconstruction application software.The software uses C#language development software,the main function is divided into input module,algorithm module and output module.The software input module reading papers to input data;operation module software is mainly to achieve a single reconstruction,the whole software module as the core part,the integration of the EHTD and EHTS algorithm can efficiently reconstruct a tetraploid haplotype;output module,four haplotypes of the reconstruction of the software is displayed in the output window,convenient data files written retained at the same time.This software refers to the rule of universal fragment data and designs fragment data module,which can be popularized.In summary,this paper studies the tetraploid haplotype reconstruction problem,and puts forward the reconstruction method effectively,design the relevant application software.The research work has certain research value for further research to lay the foundation for tetraploid species.