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网上数据库公布的棉花分子标记引物序列存在冗余性,至今也鲜见合适的软件同时分析一对引物的冗余性。为减少不同研究者的重复开发,节约时间和成本,提高对网上序列信息的利用率,借助自主开发的能同时分析一对引物和已释放的引物间是否存在冗余性的软件SSRD1.0,利用90对前人已开发的并用该软件预测过相互间存在冗余性的SSR引物,以TM-1、海7124基因组为模板分别进行扩增、电泳、测序。结果表明软件预测和基因型水平检测有88.8%的吻合度;在Identity阈值设为50%、70%时,测序结果表明序列水平和软件预测分别有75.0%、53.8%的吻合度。分别从软件预测、基因型、序列3个水平进行检测、验证,结果表明这一冗余软件和冗余性预测方法是较为有效、可行的。
There is redundancy in molecular marker primer sequences published in the online database, and so far few suitable softwares have been available to analyze the redundancy of a pair of primers at the same time. In order to reduce the repeated development of different researchers, save time and cost, improve the utilization of online sequence information, with the help of self-developed software SSRD1.0, which can simultaneously analyze whether there is redundancy between a pair of primers and released primers, Using 90 pairs of SSR primers that have been developed by predecessors and predicted by the software to have redundancy between each other, the TM-1 and Hai 7124 genomes were used as templates for amplification, electrophoresis and sequencing respectively. The results showed that there was an agreement of 88.8% between software prediction and genotype detection. When the Identity threshold was set at 50% and 70%, the sequencing results showed that the sequence level and software prediction were 75.0% and 53.8% respectively. The three levels of software prediction, genotype and sequence were tested and validated respectively. The results show that this redundancy software and redundancy prediction method are more effective and feasible.