antaRNA: ant colony-based RNA sequence design.
antaRNA: ant colony-based RNA sequence design.
复制标题
Antarna：基于蚂蚁的RNA序列设计。
DOI：
10.1093/bioinformatics/btv319
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发表时间：
2015-10-01
期刊：
影响因子：
--
通讯作者：
Backofen R
中科院分区：
文献类型：
--
作者：
Kleinkauf R;Mann M;Backofen R
动机：RNA序列设计的研究至少与经典折叠问题一样长。尽管对于后者，要找到RNA分子的功能折叠，但反向折叠试图鉴定折叠成功能特异性靶结构的RNA序列。结合基于RNA的生物技术和合成生物学，可靠的RNA序列设计成为产生新的生化成分的关键步骤。结果：在这篇文章中，提出了计算工具antaRNA。它能够编译给定结构的RNA序列，该结构还符合可调节的全范围客观GC含量分布、特定序列约束和额外的模糊结构约束。antaRNA采用蚁群优化算法，在生物数据集上显示出其上级性能。可用性和实施：http://www.bioinf.uni-freiburg.de/Software/antaRNA联系：backofen@informatik.uni-freiburg.de补充信息：补充数据可在生物信息学在线获得。
Motivation: RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found, inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology, reliable RNA sequence design becomes a crucial step to generate novel biochemical components. Results: In this article, the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution, specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. Availability and implementation: http://www.bioinf.uni-freiburg.de/Software/antaRNA Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online.