A polyhedral approach to RNA sequence structure alignment
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Edit distance between two RNA structures
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Algorithms and complexity for annotated sequence analysis
Algorithms and complexity for annotated sequence analysis
Multiple RNA Structure Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
A Binary Linear Programming Formulation of the Graph Edit Distance
IEEE Transactions on Pattern Analysis and Machine Intelligence
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The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the fourletter alphabet {A,C,G,U}. The RNA secondary and tertiary structures can be represented as a set of nested base pairs and a set of crossing base pairs, respectively. These base pairs form bonds between A - U, C - G, and G - U. This paper considers alignment with affine gap penalty between two RNA molecule structures. In general this problem is Max SNP-hard for tertiary structures. We present an algorithm for the case where aligned base pairs are non-crossing. Experimental results show that this algorithm can be used for practical application of RNA structure alignment.