RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
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DOI：
10.1093/nar/gkv460
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发表时间：
2015-07-01
影响因子：
14.9
通讯作者：
Clote P
中科院分区：
文献类型：
--
作者：
Garcia-Martin JA;Dotu I;Clote P
RNA反向折叠的几种算法已被用于设计合成核糖开关、核酶和温控开关，其活性已被实验验证。RNAiFold软件在逆折叠方法中是独特的，因为使用（穷举）约束编程而不是启发式方法。因此，RNAiFold可以生成折叠成目标结构或确定没有解决方案的所有序列。RNAiFold 2.0是对RNAiFold 1.0的彻底改造，从现已不存在的COMET语言重写为C++。新代码通过提供用户友好的管道来设计具有给定Rfam家族功能的合成结构，从而适当地扩展了其前身的功能。此外，新软件支持氨基酸限制，即使是在不同的阅读框架从重叠的编码序列翻译的蛋白质;此外，结构相容性/不相容性的限制已经扩大。通过这些功能，RNAiFold 2.0允许用户设计单个RNA分子以及两个RNA分子的杂交复合物。可用性：web服务器、源代码和Linux二进制文件可以在http://bioinformatics.bc.edu/clotelab/RNAiFold2.0上公开访问。
Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. Availability: the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0.
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影响因子：
4.1
作者：
Dotu, Ivan;Lozano, Gloria;Martinez-Salas, Encarnacion
通讯作者：
Martinez-Salas, Encarnacion
影响因子：
4.5
作者：
Grundner-Culemann, E;Martin, GW;Berry, MJ
通讯作者：
Berry, MJ
影响因子：
5.8
作者：
Busch, Anke;Backofen, Rolf
通讯作者：
Backofen, Rolf
影响因子：
2.9
作者：
MCCASKILL, JS
通讯作者：
MCCASKILL, JS
影响因子：
14.9
作者：
Garcia-Martin JA;Clote P;Dotu I
通讯作者：
Dotu I