Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm

被引：0

作者：

Shapiro, BA ^{[1
]}

Wu, JC ^{[1
]}

机构：

[1] NCI, FREDERICK CANC RES & DEV CTR, FREDERICK BIOMED SUPERCOMP CTR,SAIC FREDERICK, LECB, FREDERICK, MD 21702 USA

来源：

COMPUTER APPLICATIONS IN THE BIOSCIENCES | 1997年 / 13卷 / 04期

关键词：

D O I：

暂无

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

Motivation: Using the genetic algorithm (GA) for RNA folding on a massively parallel supercomputer, MasPar MP-2 with 16384 processors, we successfully predicted the existence of H-type pseudoknots in several sequences. Results: The GA is applied to folding the tRNA-like 3' end of turnip yellow mosaic virus (TYMV) RNA sequence with 82 nucleotides, the 3' UTRs of satellite tobacco necrosis virus (STNV)-2 RNA sequence with 619 nucleotides and STNV-1 RNA sequence with 622 nucleotides, and the bacteriophage T2, T4 and T6 gene 32 mRNA sequences with 946, 1340 and 946 nucleotides, respectively. The GA's results march the phylogenetically supported tertiary structures of these sequences.

引用

页码：459 / 471

页数：13

共 50 条

[41] OPTIMIZATION AND PERFORMANCE ANALYSIS OF A MASSIVELY-PARALLEL DYNAMIC FROG RAM MING ALGORITHM FOR RNA SECONDARY STRUCTURE PREDICTION
SHAPIRO, BA
CHEN, JH
BUSSE, T
NAVETTA, J
KASPRZAK, W
MAIZEL, JV
INTERNATIONAL JOURNAL OF SUPERCOMPUTER APPLICATIONS AND HIGH PERFORMANCE COMPUTING, 1995, 9 (01): : 29 - 39
[42] Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs
Rukov, Jakob Lewin
Hagedorn, Peter H.
Hoy, Isabel Bro
Feng, Yanping
Lindow, Morten
Vinther, Jeppe
NUCLEIC ACIDS RESEARCH, 2015, 43 (17) : 8476 - 8487
[43] Equilibrium unfolding pathway of an H-type RNA pseudoknot which promotes programmed-1 ribosomal frameshifting
Theimer, CA
Giedroc, DP
JOURNAL OF MOLECULAR BIOLOGY, 1999, 289 (05) : 1283 - 1299
[44] A permutation-based genetic algorithm for predicting RNA secondary structure - A practicable approach
Zhan, YQ
Guo, MZ
FUZZY SYSTEMS AND KNOWLEDGE DISCOVERY, PT 2, PROCEEDINGS, 2005, 3614 : 861 - 864
[45] Rapid and parallel formation of Fe3+ multimers, including a trimer, during H-type subunit ferritin mineralization
Pereira, AS
Tavares, P
Lloyd, SG
Danger, D
Edmondson, DE
Theil, EC
Huynh, BH
BIOCHEMISTRY, 1997, 36 (25) : 7917 - 7927
[46] Optimizing On-the-Fly Probability Enhanced Sampling for Complex RNA Systems: Sampling Free Energy Surfaces of an H-Type Pseudoknot
Malekzadeh, Karim
Zerze, Gu''l H.
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2025,
[47] H-Type Hypertension among Black South Africans and the Relationship between Homocysteine, Its Genetic Determinants and Estimates of Vascular Function
du Plessis, Jacomina P.
Lammertyn, Leandi
Schutte, Aletta E.
Nienaber-Rousseau, Cornelie
JOURNAL OF CARDIOVASCULAR DEVELOPMENT AND DISEASE, 2022, 9 (12)
[48] Identification of protein variants in gastrointestinal stromal tumor KIT/PDGFRA wild type (WT GISTs) with RNA massively parallel sequencing and computational analysis
Indio, V.
Tasco, G.
Martelli, P. L.
Casadio, R.
Pantaleo, M. A.
Astolfi, A.
Formica, S.
Paterini, P.
Biasco, G.
FEBS JOURNAL, 2011, 278 : 252 - 252
[49] Cascade Type H Bridge Converter on Karmonic Elimination Based on Genetic Algorithm
Zhang, Qizhe
2016 INTERNATIONAL CONFERENCE ON MECHANICAL MANUFACTURING AND ENERGY ENGINEERING (ICMMEE 2016), 2016, : 246 - 250
[50] The impact of pseudorandom number quality on P-RnaPredict, a parallel genetic algorithm for RNA secondary structure' prediction
Wiese, Kay C.
Hendriks, Andrew
Deschnes, Alain
Ben Youssef, Belgacern
GECCO 2005: GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE, VOLS 1 AND 2, 2005, : 479 - 480

← 1 2 3 4 5 →