A MASSIVELY-PARALLEL GENETIC ALGORITHM FOR RNA SECONDARY STRUCTURE PREDICTION

被引：71

作者：

SHAPIRO, BA

NAVETTA, J

机构：

[1] Image Processing Section, Laboratory of Mathematical Biology, Division of Cancer Biology, Diagnosis and Centers, National Cancer Institute, Frederick, 21702, MD, Bldg. 469

[2] Frederick Cancer Research and Development Center, National Institutes of Health, Frederick, 21702, MD, Bldg. 469

[3] Frederick Biomedical Supercomputer Center, PRI/DynCorp, NCI/FCRDC, Frederick, 21702, MD

来源：

JOURNAL OF SUPERCOMPUTING | 1994年 / 8卷 / 03期

关键词：

GENETIC ALGORITHMS; RNA STRUCTURE PREDICTION; MASSIVELY PARALLEL; DYNAMIC PROGRAMMING; OPTIMIZATION;

D O I：

10.1007/BF01204728

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

We present a new method for predicting RNA secondary structure based on a genetic algorithm. The algorithm is designed to run on a massively parallel SIMD computer. Statistical analysis shows that the program performs well when compared to a dynamic programming algorithm used to solve the same problem. The program has also pointed out a long-standing simplification in the implementation of the original dynamic programming algorithm that sometimes causes it not to find the optimal secondary structure.

引用

页码：195 / 207

页数：13

共 16 条

[1]

[Anonymous], 1987, CONNECTIONIST MACHIN

[2]

[Anonymous], 1991, FDN GENETIC ALGORITH, DOI DOI 10.1016/B978-0-08-050684-5.50008-2

[3]

Davis L. E.., 1991, HDB GENETIC ALGORITH

[4] IMPROVED FREE-ENERGY PARAMETERS FOR PREDICTIONS OF RNA DUPLEX STABILITY [J].

FREIER, SM ;

KIERZEK, R ;

JAEGER, JA ;

SUGIMOTO, N ;

CARUTHERS, MH ;

NEILSON, T ;

TURNER, DH .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1986, 83 (24) :9373-9377

[5]

Goldberg DE, 1989, GENETIC ALGORITHMS S

[6]

GOLDBERG DE, 1989, 3RD P INT C GEN ALG, P70

[7]

HOLLAND JH, 1975, ADAPTATION NATURAL A

[8] IMPROVED PREDICTIONS OF SECONDARY STRUCTURES FOR RNA [J].

JAEGER, JA ;

TURNER, DH ;

ZUKER, M .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1989, 86 (20) :7706-7710

[9]

JAEGER JA, 1990, METHODS ENZYMOL, V183, P281

[10]

SPEARS WM, 1991, FDN GENETIC ALGORITH, P301

← 1 2 →