Significance of randomness in P-RnaPredict - a parallel evolutionary algorithm for RNA folding

K.C. Wiese; A. Hendriks; A. Deschenes; B.B. Youssef; IEEE

doi:10.1109/CEC.2005.1554720

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Significance of randomness in P-RnaPredict - a parallel evolutionary algorithm for RNA folding

Conference proceeding

Peer reviewed

Significance of randomness in P-RnaPredict - a parallel evolutionary algorithm for RNA folding

K.C. Wiese, A. Hendriks, A. Deschenes, B.B. Youssef and IEEE

2005 IEEE Congress on Evolutionary Computation, Vol.1, pp.467-474 Vol.1

2005

DOI: https://doi.org/10.1109/CEC.2005.1554720

Abstract

Concurrent computing

Convergence

Evolutionary computation

Libraries

Molecular biophysics

Nuclear magnetic resonance

Predictive models

RNA

Testing

Thermodynamics

This paper presents an extension to P-RnaPredict, a parallel evolutionary algorithm (EA) for RNA folding. The impact of three pseudorandom number generators (PRNGs) on the EA's performance is evaluated. The generators tested included the C standard library PRNG RAND, a parallelized multiplicative congruential generator (MCG), and a parallelized Mersenne Twister (MT). P-RnaPredict was implemented using the message passing interface (MPI) and tested on a 128 node Beowulf cluster. The PRNG comparison testing was performed with four known structures that are 118, 122, 543, and 556 nucleotides in length. PRNGs effects were investigated and predicted structures compared to known structures

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Title: Significance of randomness in P-RnaPredict - a parallel evolutionary algorithm for RNA folding
Creators - without role: K.C. Wiese - Simon Fraser University
A. Hendriks
A. Deschenes
B.B. Youssef
IEEE
Publication Details: 2005 IEEE Congress on Evolutionary Computation, Vol.1, pp.467-474 Vol.1
Publisher: IEEE
Identifiers: 9952295808331
Academic Unit: King Saud University
Language: English
Resource Type: Conference proceeding