The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots
Abstract
Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base‐pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base‐pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1295–1304, 2004
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Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
Design and self-assembly of two-dimensional DNA crystals
Winfree, E., Liu, F., Wenzler, L. A., & Seeman, N. C. (1998) · Nature · doi:10.1038/28998 · Cited by 2,857
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Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues
Saka, S. K., Wang, Y., Kishi, J. Y., Zhu, A., Zeng, Y., Xie, W., Kirli, K., Yapp, C., Cicconet, M., Beliveau, B. J., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0207-y · Cited by 481
Understanding the transcriptome through RNA structure
Wan, Y., Kertesz, M., Spitale, R. C., Segal, E., & Chang, H. Y. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3049 · Cited by 468
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues
Kishi, J. Y., Lapan, S. W., Beliveau, B. J., West, E. R., Zhu, A., Sasaki, H. M., Saka, S. K., Wang, Y., Cepko, C. L., & Yin, P. (2019) · Nature Methods · doi:10.1038/s41592-019-0404-0 · Cited by 454
Metadata
- Authors
- Dirks, R. M., & Pierce, N. A.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2004-05-03
- Volume
- 25
- Issue
- 10
- Pages
- 1295-1304
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2163638609
- Cited by
- 171
- References
- 2
- FWCI
- 2.62
- Type
- journal article
- Language
- en
- Open access
- closed
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