Prediction of consensus structural motifs in a family of coregulated RNA sequences

Yuh-Jyh Hu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Scopus citations

Abstract

Given a set of homologous or functionally related RNA sequences, the consensus motifs may represent the binding sites of RNA regulatory proteins. Unlike DNA motifs, RNA motifs are more conserved in structures than in sequences. Knowing the structural motifs can help us gain a deeper insight of the regulation activities. There have been various studies of RNA secondary structure prediction, but most of them are not focused on finding motifs from sets of functionally related sequences. Although recent research shows some new approaches to RNA motif finding, they are limited to finding relatively simple structures, e.g. stem-loops. In this paper, we propose a novel genetic programming approach to RNA secondary structure prediction. It is capable of finding more complex structures than stem-loops. To demonstrate the performance of our new approach as well as to keep the consistency of our comparative study, we first tested it on the same data sets previously used to verify the current prediction systems. To show the flexibility of our new approach, we also tested it on a data set that contains pseudoknot motifs which most current systems cannot identify. A web-based user interface of the prediction system is set up at http://bioinfo.cis.nctu.edu.tw/service/gprm/.

Original languageEnglish
Pages (from-to)3886-3893
Number of pages8
JournalNucleic Acids Research
Volume30
Issue number17
DOIs
StatePublished - 1 Sep 2002

Fingerprint Dive into the research topics of 'Prediction of consensus structural motifs in a family of coregulated RNA sequences'. Together they form a unique fingerprint.

Cite this