Journal
NUCLEIC ACIDS RESEARCH
Volume 38, Issue 5, Pages 1711-1722Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkp1054
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Funding
- Fundacion Caja Madrid
- National Science Foundation [DBI-0543506, DMS-0817971, DMI-0600384]
- RNA Ontology Consortium
- Deutscher Akademischer Austauschdienst
- Digiteo Foundation
- Direct For Mathematical & Physical Scien
- Division Of Mathematical Sciences [0817971] Funding Source: National Science Foundation
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Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of the time required by the barriers program of Vienna RNA Package. We benchmark RNAtabupath with other algorithms to compute low energy folding pathways between experimentally known structures of several conformational switches. The RNApathfinder web server, source code for algorithms to compute and analyze pathways and supplementary data are available at http://bioinformatics.bc.edu/clotelab/RNApathfinder.
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