publication . Article . Other literature type . 2009

CentroidFold: a web server for RNA secondary structure prediction

Toutai Mituyama; Michiaki Hamada; Kiyoshi Asai; Kiyoshi Asai; Kengo Sato;
Open Access English
  • Published: 12 May 2009 Journal: Nucleic Acids Research, volume 37, issue Web Server issue, pages W277-W280 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press
Abstract
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 (...
Subjects
free text keywords: Articles, Genetics, Bioinformatics, Login, Web server, computer.software_genre, computer, Data mining, Multiple sequence alignment, Software, business.industry, business, Graph (abstract data type), Web application, Server Side Includes, Biology, Web log analysis software

Zuker, M, Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res.. 1981; 9: 133-148 [OpenAIRE] [PubMed]

Hofacker, IL. Vienna RNA secondary structure server. Nucleic Acids Res.. 2003; 31: 3429-3431 [OpenAIRE] [PubMed]

Dowell, RD, Eddy, SR. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics. 2004; 5: 71 [OpenAIRE] [PubMed]

Durbin, R, Eddy, S, Krogh, A, Mitchison, G. Biological Sequence Analysis.. 1998

Knudsen, B, Hein, J. Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res.. 2003; 31: 3423-3428 [OpenAIRE] [PubMed]

Ding, Y, Lawrence, CE. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res.. 2003; 31: 7280-7301 [OpenAIRE] [PubMed]

Ding, Y, Chan, CY, Lawrence, CE. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA. 2005; 11: 1157-1166 [OpenAIRE] [PubMed]

Carvalho, LE, Lawrence, CE. Centroid estimation in discrete high-dimensional spaces with applications in biology. Proc. Natl Acad. Sci. USA. 2008; 105: 3209-3214 [OpenAIRE] [PubMed]

Do, CB, Woods, DA, Batzoglou, S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 2006; 22: e90-e98 [OpenAIRE] [PubMed]

Hamada, M, Kiryu, H, Sato, K, Mituyama, T, Asai, K. Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics. 2009; 25: 465-473 [OpenAIRE] [PubMed]

McCaskill, JS. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 1990; 29: 1105-1119 [OpenAIRE] [PubMed]

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