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Authors:Valentin Guignon
Description:The algorithm can align a stem or a stem-loop with another stem or stem-loop. As secondary structures usually contains several stems and stem-loops. The algorithm to compaire a pair of secondary structures split both structures into stems and stem-loops and compare each pair of stems and/or stem-loops. From these comparisons, the algorithm builds a global of the two secondary structures using a Smith-Waterman algorithm where each structure is represented by a sequence of its stems and stem-loops
References:V.Guignon, C.Chauve and S.Hamel, An edit distance between RNA stem-loops, Lecture Notes in Computer Science 3772 (String Processing and Information REtrival), pp. 335-347, 2005.

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Page last modified on October 13, 2010, at 11:14 AM EST