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BMCBI
2006
158views more  BMCBI 2006»
13 years 8 months ago
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
Background: Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical s...
Andrew V. Uzilov, Joshua M. Keegan, David H. Mathe...
BMCBI
2007
143views more  BMCBI 2007»
13 years 8 months ago
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules
Background: In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular ...
Yair Horesh, Tirza Doniger, Shulamit Michaeli, Ron...
BMCBI
2004
133views more  BMCBI 2004»
13 years 7 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
HPDC
2010
IEEE
13 years 9 months ago
Exploring the RNA folding energy landscape using scalable distributed cyberinfrastructure
The increasing significance of RNAs in transcriptional or post-transcriptional gene regulation processes has generated considerable interest towards the prediction of RNA folding ...
Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed ...
BIBE
2007
IEEE
138views Bioinformatics» more  BIBE 2007»
14 years 2 months ago
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots
-We demonstrate a new algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Our approach is based on the free energy minimization criterion, and utilizes a...
Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, We...