RNA二级结构比较方法研究及基于结构的PRRSV疫苗设计

发布时间：2018-01-21 02:35

本文关键词： PRRSV ORF5 结构比较疫苗　出处：《吉林大学》2017年硕士论文　论文类型：学位论文

【摘要】：RNA作为一种生物大分子在多种生命活动过程中起着至关重要的作用。RNA的功能与其结构密切相关,结构决定了功能的变化。而RNA二级结构是RNA结构中最核心部分,是RNA一级结构与RNA三级结构间沟通的桥梁,最具保守性。因此,RNA二级结构的研究成为重要的研究方向,其结构比较也日益成为研究的焦点。猪繁殖与呼吸综合征(PRRS)会导致母猪和幼猪的死亡,传播速度快,死亡率高,对养猪业造成巨大危害。目前针对该病没有有效药物进行治疗,仅能采用注射疫苗的方式进行防治,但由于PRRSV具有高度变异性,导致疫苗在免疫效力、安全性等方面仍无法满足实际需求,在实际使用中难以推广,因此研发可靠、高效的新一代疫苗显得尤为迫切。寻找结构稳定的核心免疫RNA序列是设计PRRVS疫苗的关键。采用生物信息学手段对PRRSV的RNA进行分析,确定可能的、关键的、稳定的RNA序列,为疫苗的制备提供理论基础,是本文的研究内容。本文把计算机科学与生物信息学结合在一起,构建了一种基于结构的序列比较分析模型,并将其应用到PRRSV的分析中。模型整体流程如下所述:首先基于特征的RNA数据筛选,构建多特征筛选模型,提高数据有效性,提高处理效率,减少资源利用率。基于已记录的PRRSV的RNA数据,分别将生源地、毒性强弱以及ORF5开放阅读框等做为筛选特征,进行多次特征筛选得到目标数据集。其次采用结构比较方法对目标数据集进行比较。由于一级结构具有较高的重复,因此结构比较分析的结果更多依赖于二级结构比较,因为RNA二级结构相对于一级结构而言更加保守,更能对生物分子的功能起决定性作用。最后根据比较的结果得出了与其对应的结论,设计出相应的新型疫苗。本文的技术创新与主要的工作集中在数据筛选以及RNA二级结构比较这两方面。1、在数据筛选方面。本文选取序列长度在15000nt的初级序列;选取生源地、毒性强弱以及来源和有机体的不同作为第一次筛选的特征;由于ORF5序列在PRRSV分离株间存在高度变异性,是保守性最差的开放阅读框,选取此处数据为后续的数据处理工作提供了极大的便利,省去了许多资源浪费,因此选取ORF5开放阅读框作为第二次筛选的特征。2、建立RNA二级结构比较方法。本文基于树结构与向量的对应关系,抽象出了一种结构中点括号表示法同与其对应的向量表示方法间转换方式;设计了一种基于动态规划思想的改进的树结构的比较算法,利用向量的差异程度来查找其最大的相同子结构。本文对PRRSV分离株的RNA进行比较分析,由分析结果可知虽然一级结构相似度均在50%以上但有较高重复,无法提供理论支持。然而二级结构无重复且相似性均在0.5%以下,相似性仍然较低,但存在相似性相近的地方,表明存在部分相似结构但不是很完整,提取出这些结构可用于疫苗的设计中。
[Abstract]:As a biological macromolecule, RNA plays an important role in many life processes. The function of RNA is closely related to its structure. The RNA secondary structure is the core part of the RNA structure and the bridge between the RNA primary structure and the RNA tertiary structure, which is the most conservative. The study of RNA secondary structure has become an important research direction, and its structure comparison has increasingly become the focus of research. Porcine reproductive and respiratory syndrome (PRRSs) will lead to the death of sows and young pigs, and the transmission speed is fast. At present, there is no effective drug to treat the disease, only can be treated by injection vaccine, but because of the high variability of PRRSV. As a result, the vaccine can not meet the actual needs in immunization efficacy, safety and other aspects, so it is difficult to promote in practical use, so research and development is reliable. Efficient new generation vaccine is particularly urgent. The key to design PRRVS vaccine is to find a stable core immune RNA sequence. Bioinformatics is used to analyze the RNA of PRRSV. The identification of possible, critical and stable RNA sequences, which provide a theoretical basis for vaccine preparation, is the subject of this paper. This paper combines computer science with bioinformatics. This paper constructs a structure-based sequence comparison analysis model and applies it to the analysis of PRRSV. The overall process of the model is as follows: firstly, RNA data filtering based on features. Build multi-feature screening model to improve data efficiency, improve processing efficiency, reduce resource utilization. Based on recorded PRRSV RNA data, respectively. Toxicity and ORF5 open reading box were used as screening characteristics. The target data set is obtained by multiple feature filtering. Secondly, the target data set is compared by the structure comparison method. Because of the high repetition of the primary structure. Therefore, the results of the structural comparison analysis are more dependent on the secondary structure comparison, because the secondary structure of RNA is more conservative than the primary structure. It can play a more decisive role in the function of biomolecules. Finally, according to the results of comparison, the corresponding conclusions are obtained. The technological innovation and main work of this paper focus on data screening and RNA secondary structure comparison. 1. In the aspect of data filtering, we select the primary sequence with the length of 15000nt; The characteristics of the first screening were selected, such as the source, the toxicity, the source and the organism. Because of the high variability of ORF5 sequence among PRRSV isolates, it is the most conservative open reading box, so it is very convenient to select the data here for the subsequent data processing. A lot of waste of resources is saved, so ORF5 open reading box is selected as the feature of the second filter. The comparison method of RNA secondary structure is established. This paper based on the corresponding relationship between tree structure and vector. A transformation method between the midpoint parenthesis representation and the corresponding vector representation is presented. An improved tree structure comparison algorithm based on the idea of dynamic programming is designed to find the largest identical substructure by using the difference degree of vector. The RNA of PRRSV isolate is compared and analyzed in this paper. The results show that although the primary structure similarity is more than 50%, but has high repetition, it can not provide theoretical support. However, the secondary structure has no repetition and the similarity is below 0.5%, and the similarity is still low. But there are some similarities which indicate that there are some similar structures but not very complete. These structures can be used in vaccine design.
【学位授予单位】：吉林大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S852.4

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