CENTROIDFOLD: a web server for RNA secondary structure prediction

被引：222

作者：

Sato, Kengo ^{[1
,2
]}

Hamada, Michiaki ^{[2
,3
]}

Asai, Kiyoshi ^{[2
,4
]}

Mituyama, Toutai ^{[2
]}

机构：

[1] JBIC, Koto Ku, Tokyo 1358073, Japan

[2] Natl Inst Adv Ind Sci & Technol, CBRC, Koto Ku, Tokyo 1350064, Japan

[3] Mizuho Informat & Res Inst Inc, Chiyoda Ku, Tokyo 1018443, Japan

[4] Univ Tokyo, Grad Sch Frontier Sci, Kashiwa, Chiba 2778562, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

关键词：

CONTEXT-FREE GRAMMARS;

D O I：

10.1093/nar/gkp367

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：

The CENTROIDFOLD web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the server predicts a common secondary structure. Usage of the server is quite simple. You can paste a single RNA sequence (FASTA or plain sequence text) or a multiple alignment (CLUSTAL-W format) into the textarea then click on the 'execute CentroidFold' button. The server quickly responses with a prediction result. The major advantage of this server is that it employs our original CENTROIDFOLD software as its prediction engine which scores the best accuracy in our benchmark results. Our web server is freely available with no login requirement.

引用

页码：W277 / W280

页数：4

共 11 条

[1] Centroid estimation in discrete high-dimensional spaces with applications in biology
Carvalho, Luis E.
Lawrence, Charles E.
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (09) : 3209 - 3214
[2] RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
Ding, Y
Chan, CY
Lawrence, CE
[J]. RNA, 2005, 11 (08) : 1157 - 1166
[3] A statistical sampling algorithm for RNA secondary structure prediction
Ding, Y
Lawrence, CE
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (24) : 7280 - 7301
[4] CONTRAfold: RNA secondary structure prediction without physics-based models
Do, Chuong B.
Woods, Daniel A.
Batzoglou, Serafim
[J]. BIOINFORMATICS, 2006, 22 (14) : E90 - E98
[5] Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
Dowell, RD
Eddy, SR
[J]. BMC BIOINFORMATICS, 2004, 5 (1)
[6] Durbin R., 1998, Analysis, V356, DOI [10.1017/CBO9780511790492, DOI 10.1017/CBO9780511790492]
[7] Prediction of RNA secondary structure using generalized centroid estimators
Hamada, Michiaki
Kiryu, Hisanori
Sato, Kengo
Mituyama, Toutai
Asai, Kiyoshi
[J]. BIOINFORMATICS, 2009, 25 (04) : 465 - 473
[8] Vienna RNA secondary structure server
Hofacker, IL
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (13) : 3429 - 3431
[9] Pfold: RNA secondary structure prediction using stochastic context-free grammars
Knudsen, B
Hein, J
[J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (13) : 3423 - 3428
[10] THE EQUILIBRIUM PARTITION-FUNCTION AND BASE PAIR BINDING PROBABILITIES FOR RNA SECONDARY STRUCTURE
MCCASKILL, JS
[J]. BIOPOLYMERS, 1990, 29 (6-7) : 1105 - 1119

← 1 2 →