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BMCBI
2011
10 years 5 months ago
Structator: fast index-based search for RNA sequence-structure patterns
Background: The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching dat...
Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebas...
CORR
2006
Springer
159views Education» more  CORR 2006»
11 years 1 months ago
Structural Alignments of pseudo-knotted RNA-molecules in polynomial time
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A, C, G, U}. The higher structure i...
Michael Brinkmeier
BIOINFORMATICS
2006
130views more  BIOINFORMATICS 2006»
11 years 1 months ago
Memory efficient folding algorithms for circular RNA secondary structures
A small class of RNA molecules, in particular the tiny genomes of viroids, are circular. Yet most structure prediction algorithms handle only linear RNAs. The most straightforward ...
Ivo L. Hofacker, Peter F. Stadler
BMCBI
2007
143views more  BMCBI 2007»
11 years 1 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
2010
95views more  BMCBI 2010»
11 years 1 months ago
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA
Background: In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two de...
Emidio Capriotti, Marc A. Martí-Renom
GCB
2008
Springer
174views Biometrics» more  GCB 2008»
11 years 2 months ago
Lightweight Comparison of RNAs based on Exact Sequence-structure Matches
: Speciļ¬c functions of RNA molecules are often associated with different motifs in the RNA structure. The key feature that forms such an RNA motif is the combination of sequence ...
Steffen Heyne, Sebastian Will, Michael Beckstette,...
ICALP
2003
Springer
11 years 6 months ago
Problems on RNA Secondary Structure Prediction and Design
We describe several computational problems on prediction and design of RNA molecules.
Anne Condon
IV
2006
IEEE
108views Visualization» more  IV 2006»
11 years 7 months ago
From Visualization to Manipulation of RNA Secondary and Tertiary Structures
Ribonucleic Acid (RNA) is an important molecule which performs a wide range of functions in biological systems. We present a method for visualizing, exploring and editing RNA mole...
Gilles Bailly, David Auber, Laurence Nigay
SOFSEM
2010
Springer
11 years 10 months ago
Fast Arc-Annotated Subsequence Matching in Linear Space
An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings P and Q the arc-...
Philip Bille, Inge Li Gørtz
RECOMB
2005
Springer
12 years 1 months ago
RNA-RNA Interaction Prediction and Antisense RNA Target Search
Abstract. Recent studies demonstrating the existence of special non-coding "antisense" RNAs used in post-transcriptional gene regulation have received considerable attent...
Can Alkan, Emre Karakoç, Joseph H. Nadeau, ...
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