结合基因组变异数据的序列比对算法的分析-analysis of sequence alignment algorithm based on genome variation data.docxVIP

AbstractThe sequence alignment is of great significance for bioinformatics. With the rapid development of next-generation sequencing technology, there are vast amounts of data that could be gained for researchers in a short time. To deal with this mass of information, many alignment tools based on next-generation sequencing, which provides a great convenience to the researchers, has begun to appear. The common alignment tools operate just between single reference genome and read data, which will appeared to be inadequate in some applications. When studying the relationship of the disease and some genes ,we should align the reads from one genome to multiple genomes. Based on this consideration, the algorithm of sequence alignment which is based on HapMap database, was proposed in this paper.In this project, the topic of how to find the best match position of the read in the reference genome and the HapMap database, was divided into the followingthree cases：The best alignment position locates in common region, variation regionor union region. The BWT method was employed to align reads in common region, the equal_range algorithm was employed to align reads in variation region, and the union alignment algorithm was employed in union region.In the beginning, the background and current situation of this subject was introduced, the development process and application background of alignment algorithm was presented. Then the current mainstream alignment algorithm(BWT and Hash table) was compared and analyzed, at the meantime, the advantages and disadvantages were concluded respectively, which paved the way of our further research. Afterwards, the analysis the commonalities and differences of different genomes was completed. On this basis, the research of the HapMap sequence alignment was proposed, and the basic idea of the algorithm, technologies routes and the process were described. At last, comparing with two current popular NGS alignment tools, Bowtie and BWA, our tool