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Bioinformatics Advance Access published online on June 30, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti562
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received March 23, 2005
Revised June 25, 2005
Accepted June 27, 2005

Article

MicroRNA identification based on sequence and structure alignment

Xiaowo Wang 1 *, Jing Zhang 1 *, Fei Li 1, Jin Gu 1, Tao He 1, Xuegong Zhang 1, and Yanda Li 1*

1 MOE Key Laboratory of Bioinformatics/Department of Automation, Tsinghua University, Beijing 100084, China

* To whom correspondence should be addressed.
Yanda Li, E-mail: daulyd{at}tsinghua.edu.cn


  Abstract

Motivation: MicroRNAs (miRNA) are ~22nt long non-coding RNAs that are derived from larger hairpin RNA precursors and play important regulatory roles in both animals and plants. The short length of the miRNA sequences and relatively low conservation of pre-miRNA sequences restrict the conventional sequence-alignment-based methods to finding only relatively close homologs. On the other hand, it has been reported that miRNA genes are more conserved in secondary structure rather than primary sequences. Therefore, secondary structural features should be more fully exploited in the homologue search for new miRNA genes.

Results: In this paper, we present a novel genome-wide computational approach to detect miRNAs in animals based on both sequence and structure alignment. Experiments show this approach has higher sensitivity and comparable specificity than other reported homologue searching methods. We applied this method on Anopheles gambiae and detected 59 new miRNA genes.

Availability: This program is available at http://bioinfo.au.tsinghua.edu.cn/miralign.

Supplementary: Supplementary information is available at: http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm.

* These authors contributed equally to this work
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