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The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc(More)
Since the last ten years several tools have been proposed for RNA secondary structure pairwise comparison. These tools use different models (ordered tree or forest, arc annotated sequence, multi-level tree) and methods (edit distance, alignment). We present a first benchmark on these tools. For various RNA families, we built two sets of secondary(More)
In the last ten years, several tools have been proposed for RNA secondary structure pairwise comparison. These tools use different models (ordered tree or forest, arc annotated sequence, multi-level tree) and methods (edit distance, alignment). We present a first online benchmark for comparing these tools. For various RNA families, we built two sets of(More)
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary parsimony criterion, or, focusing on a(More)
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