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IWOCA
2010
Springer
219views Algorithms» more  IWOCA 2010»
9 years 1 months ago
Efficient Chaining of Seeds in Ordered Trees
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent wi...
Julien Allali, Cedric Chauve, Pascal Ferraro, Anne...
GCB
2010
Springer
198views Biometrics» more  GCB 2010»
9 years 4 months ago
RNALfoldz: Efficient Prediction of Thermodynamically Stable, Local Secondary Structures
Abstract: The search for local RNA secondary structures and the annotation of unusually stable folding regions in genomic sequences are two well motivated bioinformatic problems. I...
Andreas R. Gruber, Stephan H. F. Bernhart, You Zho...
NAR
2007
124views more  NAR 2007»
9 years 6 months ago
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted ...
Andreas R. Gruber, Richard Neuböck, Ivo L. Ho...
BMCBI
2004
151views more  BMCBI 2004»
9 years 6 months ago
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
Background: The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include a...
Jens Reeder, Robert Giegerich
BMCBI
2004
190views more  BMCBI 2004»
9 years 6 months ago
RAG: RNA-As-Graphs web resource
Background: The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic ...
Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie...
BMCBI
2005
306views more  BMCBI 2005»
9 years 6 months ago
A method for aligning RNA secondary structures and its application to RNA motif detection
Background: Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure a...
Jianghui Liu, Jason Tsong-Li Wang, Jun Hu, Bin Tia...
SPE
2008
91views more  SPE 2008»
9 years 6 months ago
A multiple layer model to compare RNA secondary structures
composed of various graphs linked together by relations of abstraction/refinement. The new structure is useful for representing information that can be described at t levels of abs...
Julien Allali, Marie-France Sagot
CANDC
2006
ACM
9 years 6 months ago
An RNA folding algorithm including pseudoknots based on dynamic weighted matching
On the basis of maximum weighted matching (MWM) algorithm, we introduced a dynamic weight related with stem length and used a recursive algorithm to predict RNA secondary structur...
Haijun Liu, Dong Xu, Jianlin Shao, Yifei Wang
BMCBI
2006
161views more  BMCBI 2006»
9 years 6 months ago
A method for rapid similarity analysis of RNA secondary structures
Background: Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolution...
Na Liu, Tianming Wang
CORR
2008
Springer
120views Education» more  CORR 2008»
9 years 6 months ago
A new distance for high level RNA secondary structure comparison
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the t...
Julien Allali, Marie-France Sagot
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