Cargando…

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities

BACKGROUND: It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single ‘best’ structures, and do not produce alternative structures. There are bioinformatics tools to pred...

Descripción completa

Detalles Bibliográficos
Autores principales: Hagio, Taichi, Sakuraba, Shun, Iwakiri, Junichi, Mori, Ryota, Asai, Kiyoshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836843/
https://www.ncbi.nlm.nih.gov/pubmed/29504917
http://dx.doi.org/10.1186/s12859-018-2018-4
Descripción
Sumario:BACKGROUND: It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single ‘best’ structures, and do not produce alternative structures. There are bioinformatics tools to predict suboptimal structures, but it is difficult to detect which alternative secondary structures are essential. RESULTS: We proposed a new computational method to detect essential alternative secondary structures from RNA sequences by decomposing the base-pairing probability matrix. The decomposition is calculated by a newly implemented software tool, RintW, which efficiently computes the base-pairing probability distributions over the Hamming distance from arbitrary reference secondary structures. The proposed approach has been demonstrated on ROSE element RNA thermometer sequence and Lysine RNA ribo-switch, showing that the proposed approach captures conformational changes in secondary structures. CONCLUSIONS: We have shown that alternative secondary structures are captured by decomposing base-paring probabilities over Hamming distance. Source code is available from http://www.ncRNA.org/RintW.