Smith Waterman和Jukes Cantor算法在SARS CoV-2病毒排列中的应用

T. Yulianto, Mohamad Tafrikan, R. Amalia, Emilia Yunita, Moch. Haikal, Fathorrozi Ariyanto, Zuhrotul Hasanah
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引用次数: 0

摘要

2020年初,一场始于湖北省武汉市的新型肺炎疫情震惊了世界,随后迅速蔓延到190多个国家和地区。此次疫情被命名为由严重急性呼吸综合征冠状病毒-2 (SARS-CoV-2)引起的冠状病毒病2019 (COVID-19)。这种疾病的传播产生了广泛的社会和经济影响。围绕这种疾病,包括在诊断、治疗和预防方面,仍然存在很多争议。因此,我们对2020年初至2020年3月底广泛发表的与新冠肺炎相关的研究进行了研究。因此,为了克服这个问题,史密斯沃特曼朱克斯康托算法通过采用一对DNA和RNA序列来对齐蛋白质序列来对齐covid - 19。从这种比对中,就可以知道相同和突变的百分比。遗传密码中相同的百分比将证明,尽管疾病引起的症状几乎相同,但蛋白质序列不一定相同。基于jukes cantor方法生成系统发育树的序列间距离模拟结果,得到4组26条序列分为组,即第1组16条序列,第2组6条序列,第3组2条序列,第4组2条序列。根据这些分组,发现中国武汉序列(序列MT291826)位于第1组,其他国家与中国武汉序列几乎相似,即东帝汶国家,序列MT641766也位于第1组。©2022 JNSMR UIN Walisongo。版权所有。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Application of the Smith Waterman and Jukes Cantor Algorithm in the Arrangement of the SARS CoV-2 Virus
In early 2020, the world was shocked by an outbreak of a new pneumonia that started in Wuhan, Hubei Province, which then spread rapidly to more than 190 countries and territories. This outbreak was named coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The spread of this disease has had a wide social and economic impact. There is still a lot of controversy surrounding this disease, including in the aspects of diagnosis, treatment, and prevention. Therefore, a study was carried out on studies related to COVID-19 that have been widely published since the beginning of 2020 until the end of March 2020.So to overcome this problem, the Smith Waterman Jukes Cantor Algorithm was made to align Covid19 by taking the a pair of DNA and RNA sequencesto align protein sequences. From this alignment, the percentage of identical and mutations will be known. The identical percentage in the genetic code will prove that although the symptoms caused by the disease are almost the same, the protein sequences are not necessarily the same. Based on the simulation results of the distance between sequences that produce a phylogenetic tree using the jukes cantor method, it was obtained that 4 groups of 26 sequences were divided into groups, namely, group 1 consists of 16 sequences, group 2 consists of 6 sequences, group 3 consists of 2 sequences, group 4 consists of 2 sequences. Based on these groups, it turns out that the China Wuhan sequence (sequence MT291826) is located in group 1 and other countries that are almost similar to the sequence in China Wuhan, namely the country of Timoe Leste with the sequence MT641766 also located in group 1.©2022 JNSMR UIN Walisongo. All rights reserved.
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