How to Compare Arc-Annotated Sequences: The Alignment Hierarchy
We describe a new unifying framework to express comparison of arc-annotated sequences, which we call alignment of arc-annotated sequences. We first prove that this framework encompasses main existing models, which allows us to deduce complexity results for several cases from the literature. We also show that this framework gives rise to new relevant problems that have not been studied yet. We provide a thorough analysis of these novel cases by proposing two polynomial time algorithms and an NP-completeness proof. This leads to an almost exhaustive study of alignment of arc-annotated sequences.
Keywordscomputational biology RNA structures arc-annotated sequences NP-hardness edit distance algorithm
Unable to display preview. Download preview PDF.
- 3.Blin, G., Fertin, G., Rusu, I., Sinoquet, C.: RNA sequences and the EDIT(NESTED, NESTED) problem. technical report - LINA (2003)Google Scholar
- 6.Evans, P.: Algorithms and Complexity for Annotated Sequences Analysis. PhD thesis, University of Victoria (1999)Google Scholar
- 7.Herrbach, C., Denise, A., Dulucq, S., Touzet, H.: A polynomial algorithm for comparing RNA secondary structures using a full set of operationsGoogle Scholar
- 9.Jiang, T., Lin, G., Ma, B., Zhang, K.: The longest common subsequence problem for arc-annotated sequences. Journal of Discrete Algorithms, 257–270 (2004)Google Scholar
- 11.Klein, P.: Computing the edit-distance between unrooted ordered trees. In: 6th European Symposium on Algorithms, pp. 91–102 (1998)Google Scholar
- 13.Lin, G., Ma, B., Zhang, K.: Edit distance between two rna structures. In: RECOMB, pp. 211–220 (2001)Google Scholar