Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification.
Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification.
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DOI：
10.1007/s00705-014-2197-x
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发表时间：
2014-12
影响因子：
2.7
通讯作者：
Tatusova, Tatiana
中科院分区：
文献类型：
--
作者：
Bao, Yiming;Chetvernin, Vyacheslav;Tatusova, Tatiana
公共数据库中的病毒基因组序列数量急剧增加，这些序列在病毒分类中发挥着重要作用。成对序列比较是一种基于序列的病毒分类方法。利用该方法编制的程序可以计算病毒序列在病毒科中的两两同源性并显示其分布，可视化分析有助于确定不同分类水平（如株、种、属和亚科）的界限。随后将新序列与现有序列进行比较，可以对衍生新序列的病毒进行分类。虽然这种方法在某些情况下不能作为病毒分类的唯一标准，但它是一种定量方法，与传统的病毒分类方法相比具有许多优点。它已被应用于几个病毒科，并有越来越多的兴趣使用这种方法对其他病毒科/组。配对序列比较（PASC）分类工具是在国家生物技术信息中心创建的。该工具的数据库存储了56个病毒家族/组的完整基因组/片段的成对身份。该系统的数据每天更新，以反映病毒分类的变化和公共数据库中新病毒序列的增加。该工具的网络界面（http：//www.ncbi.nlm.nih.gov/sutils/pasc/）便于导航和进行分析。该系统可同时检测多个新病毒基因组序列，以提示病毒分离株在特定家族中的分类学位置。PASC消除了由研究人员使用的不同算法和/或不同数据引起的结果中的潜在差异。
The number of viral genome sequences in the public databases is increasing dramatically, and these sequences are playing an important role in virus classification. Pairwise sequence comparison is a sequence-based virus classification method. A program using this method calculates the pairwise identities of virus sequences within a virus family and displays their distribution, and visual analysis helps to determine demarcations at different taxonomic levels such as strain, species, genus and subfamily. Subsequent comparison of new sequences against existing ones allows viruses from which the new sequences were derived to be classified. Although this method cannot be used as the only criterion for virus classification in some cases, it is a quantitative method and has many advantages over conventional virus classification methods. It has been applied to several virus families, and there is an increasing interest in using this method for other virus families/groups. The Pairwise Sequence Comparison (PASC) classification tool was created at the National Center for Biotechnology Information. The tool’s database stores pairwise identities for complete genomes/segments of 56 virus families/groups. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool (http://www.ncbi.nlm.nih.gov/sutils/pasc/) makes it easy to navigate and perform analyses. Multiple new viral genome sequences can be tested simultaneously with this system to suggest the taxonomic position of virus isolates in a specific family. PASC eliminates potential discrepancies in the results caused by different algorithms and/or different data used by researchers.
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成对序列比较（PASC）及其在丝状病毒分类中的应用。
DOI：
10.3390/v4081318
发表时间：
2012-08
期刊：
Viruses
影响因子：
--
作者：
Bao Y;Chetvernin V;Tatusova T
通讯作者：
Tatusova T
影响因子：
2.7
作者：
Muhire, Brejnev;Martin, Darren P.;Varsani, Arvind
通讯作者：
Varsani, Arvind
影响因子：
2.7
作者：
González JM;Gomez-Puertas P;Cavanagh D;Gorbalenya AE;Enjuanes L
通讯作者：
Enjuanes L
影响因子：
5.4
作者：
Oberste, MS;Maher, K;Pallansch, MA
通讯作者：
Pallansch, MA
影响因子：
5.4
作者：
Matthijnssens, Jelle;Ciarlet, Max;Van Ranst, Marc
通讯作者：
Van Ranst, Marc