Genome-Wide RNA Secondary Structure Prediction.
Methods Mol Biol
; 2586: 35-48, 2023.
Article
en En
| MEDLINE
| ID: mdl-36705897
The information of RNA secondary structure has been widely applied to the inference of RNA function. However, a classical prediction method is not feasible to long RNAs such as mRNA due to the problems of computational time and numerical errors. To overcome those problems, sliding window methods have been applied while their results are not directly comparable to global RNA structure prediction. In this chapter, we introduce ParasoR, a method designed for parallel computation of genome-wide RNA secondary structures. To enable genome-wide prediction, ParasoR distributes dynamic programming (DP) matrices required for structure prediction to multiple computational nodes. Using the database of not the original DP variable but the ratio of variables, ParasoR can locally compute the structure scores such as stem probability or accessibility on demand. A comprehensive analysis of local secondary structures by ParasoR is expected to be a promising way to detect the statistical constraints on long RNAs.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Algoritmos
/
ARN
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2023
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Estados Unidos