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12 years 17 days ago
Accelerating the Nussinov RNA folding algorithm with CUDA/GPU
Graphics processing units (GPU) on commodity video cards have evolved into powerful computational devices. The RNA secondary structure arises from the primary structure and a backb...
Dar-Jen Chang, Christopher Kimmer, Ming Ouyang
101views more  NAR 2008»
12 years 4 months ago
RNALogo: a new approach to display structural RNA alignment
Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to cr...
Tzu-Hao Chang, Jorng-Tzong Horng, Hsien-Da Huang
129views more  NAR 2007»
12 years 5 months ago
taveRNA: a web suite for RNA algorithms and applications
We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is ...
Cagri Aksay, Raheleh Salari, Emre Karakoç, ...
129views more  JCB 2000»
12 years 5 months ago
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers
We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The p...
Martin Fekete, Ivo L. Hofacker, Peter F. Stadler
108views more  BMCBI 2002»
12 years 5 months ago
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algo...
Sean R. Eddy
133views more  BMCBI 2004»
12 years 5 months ago
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
Background: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily co...
Robin D. Dowell, Sean R. Eddy
149views more  JCO 2007»
12 years 5 months ago
A 2-approximation for the preceding-and-crossing structured 2-interval pattern problem
The 2-interval pattern problem over its various models and restrictions was proposed by Vialette (2004) for the application of RNA secondary structure prediction. We present an O(n...
Minghui Jiang
141views more  JUCS 2006»
12 years 5 months ago
Constraint Based Methods for Biological Sequence Analysis
: The need for processing biological information is rapidly growing, owing to the masses of new information in digital form being produced at this time. Old methodologies for proce...
Maryam Bavarian, Verónica Dahl
108views more  JCB 2008»
12 years 5 months ago
Asymptotics of RNA Shapes
Abstract. RNA shapes, introduced by Giegerich et al. (17), provide a useful classification of the branching complexity for RNA secondary structures. In this paper, we derive an exa...
W. A. Lorenz, Yann Ponty, Peter Clote
111views more  IJBRA 2006»
12 years 5 months ago
Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots
: Stochastic Context-Free Grammars (SCFG) has been shown to be effective in modelling RNA secondary structure for searches. Our previous work (Cai et al., 2003) in Stochastic Paral...
Yinglei Song, Chunmei Liu, Russell L. Malmberg, Co...