RNAstructure: software for RNA secondary structure prediction and analysis

被引：1419

作者：

Reuter, Jessica S.

Mathews, David H. ^{[1
]}

机构：

[1] Univ Rochester, Med Ctr, Dept Biochem & Biophys, Rochester, NY 14642 USA

来源：

BMC BIOINFORMATICS | 2010年 / 11卷

基金：

美国国家卫生研究院;

关键词：

FREE-ENERGY MINIMIZATION; DOT-T MISMATCHES; NEAREST-NEIGHBOR THERMODYNAMICS; DOUBLE-HELIX FORMATION; DNA HAIRPINS; BASE-PAIRS; HYBRIDIZATION THERMODYNAMICS; PROBABILISTIC ALIGNMENT; UNPAIRED NUCLEOTIDES; SEQUENCE DEPENDENCE;

D O I：

10.1186/1471-2105-11-129

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. Results: RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. Conclusion: The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure. html.

引用

页数：9

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