Some simple computational methods to improve the folding of large RNAs
- PMID: 6198623
- PMCID: PMC320982
- DOI: 10.1093/nar/12.1part1.45
Some simple computational methods to improve the folding of large RNAs
Abstract
Computational methods are described which increase the efficiency of the RNA folding algorithm described by Zuker and Stiegler. Bit addressing has been used to reduce the memory requirements from 2NxN to NxN/2. The order in which the nucleotide sequence is examined internally has been altered, and some additional short arrays which carry temporary information have been introduced. These changes optimize the management of the large data arrays generated by the algorithm. The methods were developed for use with a UNIVAC 1100/82 computer. They are, however, easily adaptable to other computers; especially those with virtual memory capabilities. The analysis of sequences up to 1000 nucleotides long are relatively routine, and larger searches are also feasible. Some limitations and applications of the algorithm are also discussed.
Similar articles
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.Nucleic Acids Res. 1981 Jan 10;9(1):133-48. doi: 10.1093/nar/9.1.133. Nucleic Acids Res. 1981. PMID: 6163133 Free PMC article.
-
Energy directed folding of RNA sequences.Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):67-74. doi: 10.1093/nar/12.1part1.67. Nucleic Acids Res. 1984. PMID: 6198625 Free PMC article.
-
An accelerated algorithm for calculating the secondary structure of single stranded RNAs.Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):53-66. doi: 10.1093/nar/12.1part1.53. Nucleic Acids Res. 1984. PMID: 6198624 Free PMC article.
-
Heat capacity changes associated with nucleic acid folding.Biopolymers. 2006 May;82(1):38-58. doi: 10.1002/bip.20457. Biopolymers. 2006. PMID: 16429398 Free PMC article. Review.
-
Exposing the kinetic traps in RNA folding.Curr Opin Struct Biol. 1999 Jun;9(3):339-45. doi: 10.1016/S0959-440X(99)80045-1. Curr Opin Struct Biol. 1999. PMID: 10361090 Review.
Cited by
-
Structure and evolution of the 7SL RNA component of the signal recognition particle.EMBO J. 1984 Oct;3(10):2325-32. doi: 10.1002/j.1460-2075.1984.tb02134.x. EMBO J. 1984. PMID: 6209132 Free PMC article.
-
The secondary structure of a messenger RNA precursor probed with psoralen is melted in an in vitro splicing reaction.Nucleic Acids Res. 1987 Nov 25;15(22):9279-98. doi: 10.1093/nar/15.22.9279. Nucleic Acids Res. 1987. PMID: 3317279 Free PMC article.
-
A dynamic programming algorithm for finding alternative RNA secondary structures.Nucleic Acids Res. 1986 Jan 10;14(1):299-315. doi: 10.1093/nar/14.1.299. Nucleic Acids Res. 1986. PMID: 3003675 Free PMC article.
-
Two RNA species co-purify with RNase P from the fission yeast Schizosaccharomyces pombe.EMBO J. 1986 Jul;5(7):1697-703. doi: 10.1002/j.1460-2075.1986.tb04413.x. EMBO J. 1986. PMID: 3743551 Free PMC article.
-
DNA sequence of the purC gene encoding 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide synthetase and organization of the dapA-purC region of Escherichia coli K-12.J Bacteriol. 1990 Oct;172(10):6035-41. doi: 10.1128/jb.172.10.6035-6041.1990. J Bacteriol. 1990. PMID: 2120198 Free PMC article.
References
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
