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» Partition function and base pairing probabilities of RNA het...
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ALMOB
2006
47views more  ALMOB 2006»
13 years 4 months ago
Partition function and base pairing probabilities of RNA heterodimers
Stephan H. F. Bernhart, Hakim Tafer, Ulrike Mü...
JCB
2000
129views more  JCB 2000»
13 years 4 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
NAR
2010
107views more  NAR 2010»
12 years 11 months ago
PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attun...
Satish Chikkagoudar, Dennis R. Livesay, Usman Rosh...
BIBM
2008
IEEE
105views Bioinformatics» more  BIBM 2008»
13 years 11 months ago
Energy Profile and Secondary Structure Impact shRNA Efficacy
Many characteristics of functional synthetic siRNAs have been identified. Our three-phase algorithm was developed to design siRNA on a wholegenome scale based on these characteris...
Hong Zhou, Xiao Zeng
BMCBI
2010
139views more  BMCBI 2010»
13 years 5 months ago
RNAstructure: software for RNA secondary structure prediction and analysis
Background: To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of...
Jessica S. Reuter, David H. Mathews