Research And Implementation Of Smith-Waterman Algorithm's Hardware Acceleration

Bioinformatics is an area based on collection,procession,storage,spread,analysis and explanation of bioinformation's research,it's also an area with the significantly rapid development of computer science and combination between bioscience and computer science.With the help of biology,computer science and information technology,bioinfomatics reveal the biological mysteries under lots of intricate biological datas.Similarity analysis is the most original problem in bioinfomatics,and the basic method of similarity analysis is sequece alignment,using sequece alignment to make sure two or multiple sequeces' similarity or homology,with some algorithms getting final alignment results.There are 4 sequece alignments:2-sequece alignment,multiple sequece alignment,local alignment,global alignment,which invole Needleman-Wunsch algorithm for global alignment,Smith-Waterman,BLAST algorithms for local alignment.Those algorithms are extensively used in BWA,Bowtie and SOAP softwares.Over the past years,the cost of sequencing human DNA has decreased significantly for the development of Next Generation Sequencing(NGS).Lower sequencing cost leads to sequencing datas' rapid deposition,then nowtime computing resourses and computing speed can't catch up with the above datas' accumulation,there appearing the missmatch between data generation and data processing,which is focused on by this thesis.This thesis mainly discusses the Smith-Waterman algorithm 's implement and acceleration on hardware platform.Firstly,this thesis profiles the BWA-MEM tool,dig out how the BWA-MEM using the Smith-Waterman algorithm.Sencondly,discussing how chossing the acceleration hardware platform,meantime discussing the specific implement strategies.Finally,implementing the Smith-Waterman algorithm to the target hardware platform,and qualitative and quantitative analysis are necessary for this thesis' conclusion.In view of the collaboration property with the relevant company,this thesis' research achievement will be helpful to the type approval and follow-up research of the company.