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Bioinformatics Advance Access originally published online on June 30, 2005
Bioinformatics 2005 21(18):3610-3614; 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{at}oupjournals.org

MicroRNA identification based on sequence and structure alignment

Xiaowo Wang {dagger}, Jing Zhang {dagger}, Fei Li , Jin Gu , Tao He , Xuegong Zhang and Yanda Li *

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

*To whom correspondence should be addressed.

Motivation: MicroRNAs (miRNA) are ~22 nt 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 the secondary structure rather than in 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

Contact: daulyd{at}tsinghua.edu.cn

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

Received on March 23, 2005; revised on June 25, 2005; accepted on June 27, 2005

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