ISSPIT
2010
12 years 11 months ago
2010
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...
NAR
2008
13 years 3 months ago
2008
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...
NAR
2007
13 years 4 months ago
2007
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 ...
JCB
2000
13 years 4 months ago
2000
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...
BMCBI
2002
13 years 4 months ago
2002
Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algo...
BMCBI
2004
13 years 4 months ago
2004
Background: RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily co...
JCO
2007
13 years 4 months ago
2007
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...
JUCS
2006
13 years 4 months ago
2006
: 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...
JCB
2008
13 years 4 months ago
2008
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...
IJBRA
2006
13 years 4 months ago
2006
: 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...