MicroRNA identification based on sequence and structure alignment.
BACKGROUND
MicroRNAs (miRNA) are approximately 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.


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


BACKGROUND
Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm.
MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing 100084, China.
Xiaowo
X
Wang
Jing
J
Zhang
Fei
F
Li
Jin
J
Gu
Tao
T
He
Xuegong
X
Zhang
Yanda
Y
Li
D000465:Algorithms; D000818:Animals; D000852:Anopheles / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D016678:Genome; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry*; D008969:Molecular Sequence Data; D012322:RNA Precursors; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA; D012984:Software
D035683:MicroRNAs; D012322:RNA Precursors