RNAstructure: web servers for RNA secondary structure prediction and analysis

被引：299
作者：
Bellaousov, Stanislav [1 ,2 ]
Reuter, Jessica S. [1 ,2 ]
Seetin, Matthew G. [1 ,2 ]
Mathews, David H. [1 ,2 ,3 ]
机构：
[1] Univ Rochester, Med Ctr, Dept Biochem & Biophys, Rochester, NY 14642 USA
[2] Univ Rochester, Med Ctr, Ctr RNA Biol, Rochester, NY 14642 USA
[3] Univ Rochester, Med Ctr, Dept Biostat & Computat Biol, Rochester, NY 14642 USA
来源：
NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / W1期
基金：
美国国家卫生研究院;
关键词：
PROBABILISTIC ALIGNMENT; ALGORITHM; TARGET; CONSTRAINTS; DESIGN; COMMON; SIRNA;
D O I：
10.1093/nar/gkt290
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
RNAstructure is a software package for RNA secondary structure prediction and analysis. This contribution describes a new set of web servers to provide its functionality. The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot prediction. Bimolecular secondary structure prediction is also provided. Additionally, the server can predict secondary structures conserved in either two homologs or more than two homologs. Folding free energy changes can be predicted for a given RNA structure using nearest neighbor rules. Secondary structures can be compared using circular plots or the scoring methods, sensitivity and positive predictive value. Additionally, structure drawings can be rendered as SVG, postscript, jpeg or pdf. The web server is freely available for public use at: http://rna.urmc.rochester.edu/RNAstructureWeb.
引用
收藏
页码：W471 / W474
页数：4
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