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» Canonical RNA Pseudoknot Structures
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JCB
2006
126views more  JCB 2006»
13 years 7 months ago
Combinatorics of Saturated Secondary Structures of RNA
Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of s...
P. Clote
BMCBI
2010
139views more  BMCBI 2010»
13 years 7 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
BMCBI
2008
145views more  BMCBI 2008»
13 years 7 months ago
Directed acyclic graph kernels for structural RNA analysis
Background: Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel ...
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubum...
WABI
2005
Springer
120views Bioinformatics» more  WABI 2005»
14 years 1 months ago
Multiple Structural RNA Alignment with Lagrangian Relaxation
In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence ...
Markus Bauer, Gunnar W. Klau, Knut Reinert
BMCBI
2010
175views more  BMCBI 2010»
13 years 7 months ago
Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspe
Background: RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly ...
S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veerav...