Prediction of RNA base pairing probabilities on massively parallel computers

Authors
Fekete, M Hofacker, IL Stadler, PF
Citation
M. Fekete et al., Prediction of RNA base pairing probabilities on massively parallel computers, J COMPUT BI, 7(1-2), 2000, pp. 171-182
Citations number
25
Categorie Soggetti
Biochemistry & Biophysics
Journal title
JOURNAL OF COMPUTATIONAL BIOLOGY
ISSN journal
10665277 → ACNP
Volume
7
Issue
1-2
Year of publication
2000
Pages
171 - 182
Database
ISI
SICI code
1066-5277(200002/04)7:1-2<171:PORBPP>2.0.ZU;2-W
Abstract
We present an implementation of McCaskill's algorithm for computing the bas e pair probabilities of an RNA molecule for massively parallel message pass ing architectures. The program can be used to routinely fold RNA sequences of more than 10,000 nucleotides. Applications to complete viral genomes are discussed.