Towards optimally solving the longest common subsequence problem for sequences with nested arc annotations in linear time, Proc. of the 13th Symposium on Combinatorial Pattern Matching (CPM02), volume 2373 of LNCS, pp.99-114, 2002. ,
Computing the similarity of two sequences with nested arc annotations, Theoretical Computer Science, vol.312, issue.2-3, pp.337-358, 2004. ,
DOI : 10.1016/j.tcs.2003.10.026
Cirripede Phylogeny Using a Novel Approach: Molecular Morphometrics, Molecular Biology and Evolution, vol.17, issue.10, pp.138-148, 2000. ,
DOI : 10.1093/oxfordjournals.molbev.a026244
Tracing the evolution of RNA structure in ribosomes, Nucleic Acids Research, vol.30, issue.11, pp.2575-2587, 2002. ,
DOI : 10.1093/nar/30.11.2575
RNA sequence requirements for NasR-mediated, nitrate-responsive transcription antitermination of the Klebsiella oxytoca M5al nasF operon leader, Journal of Molecular Biology, vol.292, issue.2, pp.203-216, 1999. ,
DOI : 10.1006/jmbi.1999.3084
Algorithms and Complexity for Annotated Sequence Analysis, 1999. ,
Finding Common Subsequences with Arcs and Pseudoknots, Proc. of the 10th Symposium Combinatorial Pattern Matching (CPM99), pp.270-280, 1999. ,
DOI : 10.1007/3-540-48452-3_20
Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis, Nucleic Acids Research, vol.27, issue.4, pp.1070-1078, 1999. ,
DOI : 10.1093/nar/27.4.1070
Computers and Intractability: A Guide to the Theory of NP-Completeness, 1979. ,
Algorithmic aspects of protein structure similarity, 40th Annual Symposium on Foundations of Computer Science (Cat. No.99CB37039), pp.512-522, 1999. ,
DOI : 10.1109/SFFCS.1999.814624
Pattern matching for arc-annotated sequences, Proc. of the 22nd Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS02), volume 2556 of LNCS, pp.182-193, 2002. ,
DOI : 10.1145/1125994.1125997
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.13.7716
Exact algorithms for the longest common subsequence problem for arcannotated sequences, 2002. ,
Protonatable Hairpins Are Conserved in the 5'-Untranslated Region of Tymovirus RNAs, Nucleic Acids Research, vol.24, issue.24, pp.4910-4917, 1996. ,
DOI : 10.1093/nar/24.24.4910
Automatic detection of conserved RNA structure elements in complete RNA virus genomes, Nucleic Acids Research, vol.26, issue.16, pp.3825-3836, 1998. ,
DOI : 10.1093/nar/26.16.3825
The longest common subsequence problem for arc-annotated sequences, Proc. 11th Symposium on Combinatorial Pattern Matching (CPM00), volume 1848 of LNCS, pp.154-165, 2000. ,
Evidence for evolutionarily conserved secondary structure in the H19 tumor suppressor RNA, Nucleic Acids Research, vol.28, issue.5, pp.1221-1227, 2000. ,
DOI : 10.1093/nar/28.5.1221
101 optimal PDB structure alignments, Proceedings of the fifth annual international conference on Computational biology , RECOMB '01, pp.193-202, 2001. ,
DOI : 10.1145/369133.369199
Conserved features of Y RNAs: a comparison of experimentally derived secondary structures, Nucleic Acids Research, vol.28, issue.2, pp.610-619, 2000. ,
DOI : 10.1093/nar/28.2.610
Pattern Matching Problems over 2-Interval Sets, Proc. 13th Annual Symposium Combinatorial Pattern Matching (CPM02), pp.53-63, 2002. ,
DOI : 10.1007/3-540-45452-7_6
On the computational complexity of 2-interval pattern matching problems, Theoretical Computer Science, vol.312, issue.2-3, pp.223-249, 2004. ,
DOI : 10.1016/j.tcs.2003.08.010
Secondary Structure of Mitochondrial 12S rRNA Among Fish and Its Phylogenetic Applications, Molecular Biology and Evolution, vol.19, issue.2, pp.138-148, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004066
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA, Nucleic Acids Research, vol.28, issue.23, pp.4698-4708, 2000. ,
DOI : 10.1093/nar/28.23.4698
Computing Similarity between RNA Structures, Proc. 10th Symposium on Combinatorial Pattern Matching (CPM99), pp.281-293, 1999. ,
DOI : 10.1007/3-540-48452-3_21
[20] Computer prediction of RNA structure, RNA folding. Meth. Enzymology, vol.180, pp.262-288, 1989. ,
DOI : 10.1016/0076-6879(89)80106-5