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» Normalized Similarity of RNA Sequences
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JCB
2002
111views more  JCB 2002»
13 years 7 months ago
A General Edit Distance between RNA Structures
Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of ne...
Tao Jiang, Guohui Lin, Bin Ma, Kaizhong Zhang
RECOMB
2006
Springer
14 years 7 months ago
RNA Secondary Structure Prediction Via Energy Density Minimization
Abstract. There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding R...
Can Alkan, Emre Karakoç, Süleyman Cenk...
RECOMB
2001
Springer
14 years 7 months ago
A new approach to sequence comparison: normalized sequence alignment
The Smith-Waterman algorithm for local sequence alignment is one of the most important techniques in computational molecular biology. This ingenious dynamic programming approach w...
Abdullah N. Arslan, Ömer Egecioglu, Pavel A. ...
WG
2005
Springer
14 years 25 days ago
Fixed-Parameter Algorithms for Protein Similarity Search Under mRNA Structure Constraints
Abstract. In the context of protein engineering, we consider the problem of computing an mRNA sequence of maximal codon-wise similarity to a given mRNA (and consequently, to a give...
Guillaume Blin, Guillaume Fertin, Danny Hermelin, ...
GCB
2008
Springer
174views Biometrics» more  GCB 2008»
13 years 8 months ago
Lightweight Comparison of RNAs based on Exact Sequence-structure Matches
: Specific 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,...