Efficient computation of optimal oligo-RNA binding.
Nucleic Acids Res
; 32(22): 6636-42, 2004.
Article
em En
| MEDLINE
| ID: mdl-15608295
ABSTRACT
We present an algorithm that calculates the optimal binding conformation and free energy of two RNA molecules, one or both oligomeric. This algorithm has applications to modeling DNA microarrays, RNA splice-site recognitions and other antisense problems. Although other recent algorithms perform the same calculation in time proportional to the sum of the lengths cubed, O((N1 + N2)3), our oligomer binding algorithm, called bindigo, scales as the product of the sequence lengths, O(N1*N2). The algorithm performs well in practice with the aid of a heuristic for large asymmetric loops. To demonstrate its speed and utility, we use bindigo to investigate the binding proclivities of U1 snRNA to mRNA donor splice sites.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Oligorribonucleotídeos
/
Algoritmos
/
Análise de Sequência de RNA
/
Biologia Computacional
Tipo de estudo:
Evaluation_studies
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2004
Tipo de documento:
Article
País de afiliação:
Estados Unidos