RNAstructure: web servers for RNA secondary structure prediction and analysis

被引：284

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

页码：W471 / W474

页数：4

共 42 条

[1] The expanding snoRNA world
Bachellerie, JP
Cavaillé, J
Hüttenhofer, A
[J]. BIOCHIMIE, 2002, 84 (08) : 775 - 790
[2] ProbKnot: Fast prediction of RNA secondary structure including pseudoknots
Bellaousov, Stanislav
Mathews, David H.
[J]. RNA, 2010, 16 (10) : 1870 - 1880
[3] The promises and pitfalls of RNA-interference-based therapeutics
Castanotto, Daniela
Rossi, John J.
[J]. NATURE, 2009, 457 (7228) : 426 - 433
[4] Accurate SHAPE-directed RNA structure determination
Deigan, Katherine E.
Li, Tian W.
Mathews, David H.
Weeks, Kevin M.
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (01) : 97 - 102
[5] A statistical sampling algorithm for RNA secondary structure prediction
Ding, Y
Lawrence, CE
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (24) : 7280 - 7301
[6] The chemical repertoire of natural ribozymes
Doudna, JA
Cech, TR
[J]. NATURE, 2002, 418 (6894) : 222 - 228
[7] Interpreting oligonucleotide microarray data to determine RNA secondary structure:: Application to the 3′ end of Bombyx mori R2 RNA
Duan, Shenghua
Mathews, David H.
Turner, Douglas H.
[J]. BIOCHEMISTRY, 2006, 45 (32) : 9819 - 9832
[8] lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements
Gong, Chenguang
Maquat, Lynne E.
[J]. NATURE, 2011, 470 (7333) : 284 - +
[9] The Vienna RNA Websuite
Gruber, Andreas R.
Lorenz, Ronny
Bernhart, Stephan H.
Neuboeck, Richard
Hofacker, Ivo L.
[J]. NUCLEIC ACIDS RESEARCH, 2008, 36 : W70 - W74
[10] Recent Advances in Developing Small Molecules Targeting RNA
Guan, Lirui
Disney, Matthew D.
[J]. ACS CHEMICAL BIOLOGY, 2012, 7 (01) : 73 - 86

← 1 2 3 4 5 →