Home LiteratureArticle Details
PMID: 10648793 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Prediction of common secondary structures of RNAs: a genetic algorithm approach.

Nucleic acids research ·Vol. 28 ·No. 4 ·2000-02-15 ·Pages 991-9

Chen JH, Le SY, Maizel JV

Abstract

In this study we apply a genetic algorithm to a set of RNA sequences to find common RNA secondary structures. Our method is a three-step procedure. At the first stage of the procedure for each sequence, a genetic algorithm is used to optimize the structures in a population to a certain degree of stability. In this step, the free energy of a structure is the fitness criterion for the algorithm. Next, for each structure, we define a measure of structural conservation with respect to those in other sequences. We use this measure in a genetic algorithm to improve the structural similarity among sequences for the structures in the population of a sequence. Finally, we select those structures satisfying certain conditions of structural stability and similarity as predicted common structures for a set of RNA sequences. We have obtained satisfactory results from a set of tRNA, 5S rRNA, rev response elements (RRE) of HIV-1 and RRE of HIV-2/SIV, respectively.

MeSH Terms
Algorithms Base Sequence Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry,genetics Sequence Homology, Nucleic Acid
Chemicals
RNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Chen J H
Advanced Biomedical Computing Center, SAIC, NCI/FCRDC, Frederick, MD 21702, USA. chen@ncifcrf.gov
Le S Y
Maizel J V
References (18)
18 references, click to expand
  1. Extensive sequence-specific information throughout the CAR/RRE, the target sequence of the human immunodeficiency virus type 1 Rev protein.
    J Virol. 1992 Feb;66(2):1139-51 PMID: 1731093
  2. Common structures of the 5' non-coding RNA in enteroviruses and rhinoviruses. Thermodynamical stability and statistical significance.
    J Mol Biol. 1990 Dec 5;216(3):729-41 PMID: 2175364
  3. RNA sequence analysis using covariance models.
    Nucleic Acids Res. 1994 Jun 11;22(11):2079-88 PMID: 8029015
  4. The computer simulation of RNA folding pathways using a genetic algorithm.
    J Mol Biol. 1995 Jun 30;250(1):37-51 PMID: 7541471
  5. A genetic algorithm to search for optimal and suboptimal RNA secondary structures.
    Biophys Chem. 1995 Aug;55(3):253-9 PMID: 7542936
  6. "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA.
    Nucleic Acids Res. 1995 Jul 25;23(14):2791-8 PMID: 7544463
  7. Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein.
    J Mol Biol. 1996 May 24;258(5):813-26 PMID: 8637012
  8. An annealing mutation operator in the genetic algorithms for RNA folding.
    Comput Appl Biosci. 1996 Jun;12(3):171-80 PMID: 8872384
  9. Alignment of possible secondary structures in multiple RNA sequences using simulated annealing.
    Comput Appl Biosci. 1996 Aug;12(4):259-67 PMID: 8902352
  10. Finding the most significant common sequence and structure motifs in a set of RNA sequences.
    Nucleic Acids Res. 1997 Sep 15;25(18):3724-32 PMID: 9278497
  11. RAGA: RNA sequence alignment by genetic algorithm.
    Nucleic Acids Res. 1997 Nov 15;25(22):4570-80 PMID: 9358168
  12. Automatic detection of conserved RNA structure elements in complete RNA virus genomes.
    Nucleic Acids Res. 1998 Aug 15;26(16):3825-36 PMID: 9685502
  13. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
    J Mol Biol. 1999 May 21;288(5):911-40 PMID: 10329189
  14. The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA.
    Nature. 1989 Mar 16;338(6212):254-7 PMID: 2784194
  15. Computer analysis of nucleic acid sequences.
    Methods Enzymol. 1988;164:765-93 PMID: 3071692
  16. On finding all suboptimal foldings of an RNA molecule.
    Science. 1989 Apr 7;244(4900):48-52 PMID: 2468181
  17. A highly conserved RNA folding region coincident with the Rev response element of primate immunodeficiency viruses.
    Nucleic Acids Res. 1990 Mar 25;18(6):1613-23 PMID: 2326200
  18. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.
    Microbiol Rev. 1994 Mar;58(1):10-26 PMID: 8177168
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/28.4.991
Email
chen@ncifcrf.gov
Published
2000-02-15
Pages
991-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC102574
Subset
IM
Grants
NCI NIH HHS · N01-CO-56000 · United States
Databases
GENBANK
D00835, J03654, J04498, J04542, L07625, M15390, M16403, M19499, M30502, M31113
External Links
PubMed source DOI: 10.1093/nar/28.4.991 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2