【摘要】 为扩大MISA工具(MIcro SAtellite identification tool)的适用范围,本研究尝试用MISA对其他类型的序列进行分析,探讨关键参数对分析结果的影响。研究收集了5种类型的甜菜序列数据,探讨了不同类型序列适用的相关分析参数,以及不同参数对分析结果的影响。利用MISA工具分析了5种类型的甜菜序列,其中4种来自公共数据库,1种来自课题组前期工作。结果表明在适当的参数下,配合适当的序列库格式化处理,MISA可以应用于不同的甜菜序列类型。可分析的序列库长度上限取决于去冗余工具的要求,并影响去冗余处理的时间和结果,重复单元长度的限定参数影响位点挖掘数量和引物设计成功率,序列长度的分布范围不影响分析。应用参数调整后的脚本,从5种甜菜序列库中共挖掘出了SSR标记位点约8000个。可知MISA的应用范围可以扩展,需要调整的关键参数包括2项:序列库的长度上限与重复单元长度。建议序列长度在程序与硬件允许的情况下尽量长,重复单元长度根据研究目标调整。更多还原

【Abstract】 This work aims to extend the application range of MISA(MIcro SAtellite identification tool). The authors adjusted important parameters of MISA to find their effects on analysis results, and attempted to applyMISA to analyze other sequence types. Five different types of sequences of Beta vulgaris were collected andanalyzed to find out appropriate parameters for each sequence type, and to clarify the effects of differentparameters on analysis results. Among the five types of sequences, four were collected from public databaseand one was obtained from the early work of the research team. MISA was found to be able to analyze all thesefive sequence types of B. vulgaris sequences with appropriate analyzing parameters and sequence format. Themax length of the sequence library was restricted by the redundant sequence removing tools, and affected redundant sequence processing, including both time consumption and analysis results. The length of detectablerepeat units affected the amount of mined sites and the designing of primers. The length range of the sequencelibrary did not disturb MISA analysis. About 8000 SSR sites were mined from the five types of B. vulgaris sequences using MISA tool with adjusted parameters. These results implied that MISA could be applied toanalyzing different sequence types. Two parameters, the limit of sequence max length in the sequence pool andthe length of detectable repeat units, should be adjusted. It is suggested that the sequences should be as long aspossible under the permission of hardware and software, the length of repeat units should be adjusted according to the research purpose.更多还原