Sfold web server for statistical folding and rational design of nucleic acids
Sfold web server for statistical folding and rational design of nucleic acids
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DOI：
10.1093/nar/gkh449
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Lawrence, CE
中科院分区：
文献类型：
--
作者：
Ding, Y;Chan, CY;Lawrence, CE
Sfold网络服务器通过万维网（WWW）为用户提供了对Sfold的友好访问途径，Sfold是一个近期开发的核酸折叠软件包。该软件基于一种新的用于预测RNA二级结构的统计抽样范例。此软件的主要目标之一是为合理设计靶向RNA的核酸提供计算工具，其中包括用于基因敲低研究的小干扰RNA（siRNAs）、反义寡核苷酸和反式切割核酶。siRNA设计方法基于RNA靶点可及性预测、siRNA双链热力学性质以及经验设计规则的结合。我们的靶点可及性评估方法是对基础RNA折叠算法的一种独创扩展，以考虑到靶mRNA可能存在的多种结构。除了分别用于siRNAs、反义寡核苷酸和核酶的应用模块Sirna、Soligo和Sribo之外，模块Srna为抽样结构的统计呈现提供了全面的功能。所有模块都提供图形和文本格式的详细输出。Sfold服务器可在http://sfold.wadsworth.org和http://www.bioinfo.rpi.edu/applications/sfold获取。
The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical sampling paradigm for the prediction of RNA secondary structure. One of the main objectives of this software is to offer computational tools for the rational design of RNA-targeting nucleic acids, which include small interfering RNAs (siRNAs), antisense oligonucleotides and trans-cleaving ribozymes for gene knock-down studies. The methodology for siRNA design is based on a combination of RNA target accessibility prediction, siRNA duplex thermodynamic properties and empirical design rules. Our approach to target accessibility evaluation is an original extension of the underlying RNA folding algorithm to account for the likely existence of a population of structures for the target mRNA. In addition to the application modules Sirna, Soligo and Sribo for siRNAs, antisense oligos and ribozymes, respectively, the module Srna offers comprehensive features for statistical representation of sampled structures. Detailed output in both graphical and text formats is available for all modules. The Sfold server is available at http://sfold.wadsworth.org and http://www.bioinfo.rpi.edu/applications/sfold.