Title: Detecting and assessing conserved stems for building structural alignment of RNA sequences

Authors: Xiaoyong Fang, Zhigang Luo, Bo Yuan, Zheng-Hua Wang

Addresses: National Laboratory for Parallel and Distributed Processing, National University of Defense Technology, Yanwachi Street, Deya Road, 410073 Changsha, China. ' National Laboratory for Parallel and Distributed Processing, National University of Defense Technology, Yanwachi Street, Deya Road, 410073 Changsha, China. ' Department of Biomedical Informatics, College of Medicine and Public Health, Ohio State University Columbus, 43210-1239 Ohio, USA. ' National Laboratory for Parallel and Distributed Processing, National University of Defense Technology, Yanwachi Street, Deya Road, 410073 Changsha, China

Abstract: The comparative methods for identifying non-coding RNAs or predicting RNA secondary structure can be facilitated by taking structural alignments of homologous sequences as input. However, it is very difficult to build a well structural alignment without knowing the secondary structures. Here, we propose a new method for building structural alignment of RNA sequences by detecting and assessing conserved stems across the sequences. The method can be summarised by: we detect conserved stems across multiple RNA sequences using the so-called position matrix with which some common paired positions are uncovered; we assess the conserved stems using the Signal-to-Noise and the profile SCFG; we build the structural alignment by incorporating some compatible conserved stems with the initial sequence alignment built by Clustal W. Experimental results show that our method can build structural alignment of RNA sequences with much greater sensitivity and specificity than Clustal W.

Keywords: position matrix; conserved stems; structural alignment; RNA sequences; non-coding RNAs.

DOI: 10.1504/IJFIPM.2008.021391

International Journal of Functional Informatics and Personalised Medicine, 2008 Vol.1 No.3, pp.269 - 284

Published online: 22 Nov 2008 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article