Structural alignment of large—size proteins via lagrangian relaxation
Proceedings of the sixth annual international conference on Computational biology
Finding Common Subsequences with Arcs and Pseudoknots
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Alignment of RNA base pairing probability matrices
Bioinformatics
Fast and accurate structural RNA alignment by progressive lagrangian optimization
CompLife'05 Proceedings of the First international conference on Computational Life Sciences
Multiple structural RNA alignment with lagrangian relaxation
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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RNA is generally a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to structure formation In comparing different homologous RNA molecules it is usually not sufficient to consider only the primary sequence, but it is important to consider both the sequence and the structure of the molecules Traditional alignment algorithms can only account for the sequence of bases, but not for the base pairings Considering the structure leads to significant computational problems because of the dependencies introduced by the base pairings and the presence of pseudoknots In this paper we address the problem of optimally aligning two given RNA sequences either with or without known structure (allowing for pseudoknots) We phrase the problem as an integer linear program and then solve it using Lagrangian relaxation In our computational experiments we could align large problem instances—18S and 23S ribosomal RNA with up to 1500 bases within minutes while preserving pseudoknots.