Title :
A Practical Edit-Distance Model for RNA Secondary-Structure Comparison
Author :
Wu, Chan-Shuo ; Huang, Guan-Shieng
Author_Institution :
Dept. of Comput. Sci. & Inf. Eng., Nat. Chi Nan Univ., Nantou, Taiwan
Abstract :
We point out the importance to incorporate affine-gap penalties in RNA secondary-structure comparison. Two notions of affine-gap penalties, one for sequences and the other for structures, are developed. A model from Jiang et al. in [JComput Biol, 2002, 9, (2), pp. 371-388] is extended to allow this facility, and a polynomial-time algorithm is provided in this paper. Experimental results in this paper revealed that our new model generates more accurate and biological meaningful alignments than several existing algorithms.
Keywords :
bioinformatics; macromolecules; molecular biophysics; polynomials; RNA secondary-structure comparison; affine-gap penalty; data representation; edit-distance model; polynomial-time algorithm; Bioinformatics; Biological system modeling; Biology computing; Biomedical computing; Biomedical engineering; Computer science; Costs; Polynomials; RNA; Tree data structures;
Conference_Titel :
Bioinformatics and BioEngineering, 2009. BIBE '09. Ninth IEEE International Conference on
Conference_Location :
Taichung
Print_ISBN :
978-0-7695-3656-9
DOI :
10.1109/BIBE.2009.27
