ASPRAlign：一种用于对齐具有任意假结的 RNA 二级结构的工具。
ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots.
机构信息
Department of Information Engineering, University of Padua, Padova 35131, Italy.
School of Sciences and Technology, University of Camerino, Camerino 62032, Italy.
出版信息
Bioinformatics. 2020 Jun 1;36(11):3578-3579. doi: 10.1093/bioinformatics/btaa147.
SUMMARY
Current methods for comparing RNA secondary structures are based on tree representations and exploit edit distance or alignment algorithms. Most of them can only process structures without pseudoknots. To overcome this limitation, we introduce ASPRAlign, a Java tool that aligns particular algebraic tree representations of RNA. These trees neglect the primary sequence and can handle structures with arbitrary pseudoknots. A measure of comparison, called ASPRA distance, is computed with a worst-case time complexity of O(n2) where n is the number of nucleotides of the longer structure.
AVAILABILITY AND IMPLEMENTATION
ASPRAlign is implemented in Java and source code is released under the GNU GPLv3 license. Code and documentation are freely available at https://github.com/bdslab/aspralign.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
目前用于比较 RNA 二级结构的方法基于树表示，并利用编辑距离或比对算法。大多数方法只能处理没有假结的结构。为了克服这一限制，我们引入了 ASPRAlign，这是一个用于比对 RNA 特殊代数树表示的 Java 工具。这些树忽略了原始序列，可以处理具有任意假结的结构。我们计算了一种称为 ASPRA 距离的比较度量，其时间复杂度最坏情况下为 O(n2)，其中 n 是较长结构的核苷酸数。
可用性和实现
ASPRAlign 是用 Java 实现的，并在 GNU GPLv3 许可证下发布源代码。代码和文档可在 https://github.com/bdslab/aspralign 上免费获取。
联系人
补充信息
补充数据可在 Bioinformatics 在线获得。
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