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List of the included softwares for RNA secondary structure pairwise comparison

Below is a list of softwares for RNA pairwise secondary structure comparison that are already included in Brasero. Click on the title to access to the dedicated tool page.


Authors:Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet
Description:Gardenia is a software tool for comparing and aligning RNA structures. The algorithm takes into account both the primary structure and the secondary structure to build a good multiple alignment.
References:Alignment of RNA structures, 2008

MiGal: MultIple GrAph Layers

Authors:J. Allali and M-F. Sagot
Description:Pairwise secondary structure comparison based on an edit distance algorithm using a multi-level modelling of the structures
References:A new distance for high level RNA secondary structure comparison, 2005
 A multiple layer model to compare RNA secondary structures, 2008




Authors:Walter Fontana, Ivo L Hofacker, Peter F Stadler.
Description:RNAdistance reads RNA secondary structures from stdin and calculates one or more measures for their dissimilarity, based on tree or string editing (alignment). In addition it calculates a "base pair distance" given by the number of base pairs present in one structure, but not the other. For structures of different length base pair distance is not recommended.
References:Shapiro B A, (1988) An algorithm for comparing multiple RNA secondary structures, CABIOS 4, 381-393
 Shapiro B A, Zhang K (1990) Comparing multiple RNA secondary structures using tree comparison, CABIOS 6, 309-318
 Fontana W, Konings D A M, Stadler P F, Schuster P, (1993) Statistics of RNA secondary structures, Biopolymers 33, 1389-1404
 I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125, 167-188



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.


Authors:A. Ouangraoua and P. Ferraro
References:A. Ouangraoua, P. Ferraro, L. Tichit, S. Dulucq Local similarity between quotiented ordered trees, Journal of Discrete Algorithms 2007

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Page last modified on December 09, 2010, at 03:23 PM EST