The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems
Abstract
The alignment of finite sequences, the inference of ribonucleic acid secondary structures (folding), and the reconstruction of ancestral sequences on a phylogenetic tree, are three problems which have dynamic programming solutions, which we formulate in a common mathematical framework. Combining the objective functions for alignment (parsimony, or minimal mutations) and folding (free energy), we present an algorithm which solves all three problems simultaneously for a set of N sequences of length n in time proportional to $n^{3N} $ and storage $n^{2N} $. Incorporating a “cutting corners” constraint against biologically unlikely alignments reduces these requirements so that they are proportional to $n^{3} $ and $n^{2} $, respectively, for fixed N.
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Cites
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Cited by
Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2011) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-6-26 · Cited by 5,098
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
Will, S., Reiche, K., Hofacker, I. L., Stadler, P. F., & Backofen, R. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030065 · Cited by 499
[20] Computer prediction of RNA structure
Zuker, M. (1989) · Methods in Enzymology · doi:10.1016/0076-6879(89)80106-5 · Cited by 388
RNA Pseudoknot Prediction in Energy-Based Models
Lyngsø, R. B., & Pedersen, C. N. S. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050862 · Cited by 359
Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
Will, S., Reiche, K., Hofacker, I. L., Stadler, P. F., & Backofen, R. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030065.eor · Cited by 322
Metadata
- Authors
- Sankoff, D.
- Venue
- SIAM Journal on Applied Mathematics
- Published
- 1985-10
- Volume
- 45
- Issue
- 5
- Pages
- 810-825
- ISSN
- 0036-1399 (ISSN-L)
- 1095-712X
- OpenAlex
- W2095145214
- Cited by
- 530
- References
- 1
- FWCI
- 0.29
- Type
- journal article
- Language
- en
- Open access
- closed
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