【作者】 邓志超；

【导师】 林和平；

【作者基本信息】 东北师范大学 ， 计算机应用技术， 2007， 硕士

【摘要】 比较是科学研究中最常见的方法,通过将研究对象相互比较来寻找对象可能具备的特性。在生物信息学研究中,比较多个生物序列相似性的任务是由序列比对来完成的。序列比对可用于蛋白质的功能域识别、二级结构预测、基因识别以及分子系统发育分析等方面的研究。多重序列比对有时用来区分一组序列之间的差异,但其主要用于描述一组序列之间的相似性关系,以便对一个基因家族的特征有一个简明扼要的了解。随着生物序列数据库中序列数据的激增,开发出适合大规模序列比对运算的并行算法非常迫切。本文研究了生物信息学中的多重序列比对算法以及其并行算法,主要研究内容和取得的成果如下:1.对经典的多重序列比对算法:动态规划算法和CLUSTAL算法及隐马尔可夫模型多重序列比对算法进行了研究。对几种算法的性能进行了比较和评估。2.研究了目前主流的并行计算技术,选用工作站机群技术做为本课题并行平台。提出了基于并行隐马尔可夫模型的多重序列比对算法。3.以本文提出的算法为基础,利用Microsoft Visual C++.Net开发工具设计并实现了一个基于Windows操作系统的多重序列比对的并行计算平台。4.采用几种生物一组相似蛋白质序列作为测试数据对算法进行测试,并与经典多重序列比对方法进行对比分析,结果表明基于并行隐马尔可夫模型的多重序列比对算法在解决蛋白质多重序列比对问题上是有效的,但是也存在一定的问题。最后论述了并行隐马尔可夫模型算法在序列分析方面的发展前景。更多还原

【Abstract】 Compare is the common method of research in science, by conmare the study object to identify some feature on it.In the study of bioinformatics, comparing various biological sequence similarities is mandated by the sequence alignment. Sequence alignment is used to research of the domain protein identification, secondary structure prediction, gene identification, and molecular phylogenetic analysis. Multiple sequence alignment sometimes used to distinguish a set of sequences differences, but its main used to describe a set of sequences similarity relationship for concise understanding of a gene family features. With biological sequence datas surge increase, developed for a larger sequences alignment of parallel computation algorithm is an urgent task. This paper studies the multiple sequence alignment algorithms and its parallel algorithm in bioinformatics.The main contents and results are as follows listed:1. For the classic multiple sequence alignment algorithm, study the dynamic programming algorithm and CLUSTAL programming and HMM algorithm.Make comparison and assessment for the performance on several algorithms.2. Study of the current main parallel computing technology, select Cluster Workstations for this paper as a technical platform for parallel compute.Give a multiple sequences alignment algorithm based on the parallel Hidden Markov Model.3. Base on the algorithm of this paper bring forward, design and implement a parallel computing platform based on Windows operation system by Microsoft VisualC++.net.4. Using a group of several similar biological protein sequence data for testing algorithm, comparative analysis with the classical multiple sequence alignment method. The results show that based on parallel HMM multiple sequence alignment algorithms to solve protein multiple sequence alignment problems is effective, but there are also some problems. Finally, the paper discuss the foreground of parallel HMM algorithm sequence analysis.更多还原