MicroRNA identification based on sequence and structure alignment

被引：196

作者：

Wang, XW ^{[1
]}

Zhang, J ^{[1
]}

Gu, J ^{[1
]}

He, T ^{[1
]}

Zhang, XG ^{[1
]}

Li, YD ^{[1
]}

Li, F ^{[1
]}

机构：

[1] Tsinghua Univ, Dept Automat, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China

来源：

BIOINFORMATICS | 2005年 / 21卷 / 18期

基金：

中国国家自然科学基金;

关键词：

D O I：

10.1093/bioinformatics/bti562

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: MicroRNAs (miRNA) are similar to 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.

引用

页码：3610 / 3614

页数：5

共 36 条

[31] Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA [J].

Pasquinelli, AE ;

Reinhart, BJ ;

Slack, F ;

Martindale, MQ ;

Kuroda, MI ;

Maller, B ;

Hayward, DC ;

Ball, EE ;

Degnan, B ;

Müller, P ;

Spring, J ;

Srinivasan, A ;

Fishman, M ;

Finnerty, J ;

Corbo, J ;

Levine, M ;

Leahy, P ;

Davidson, E ;

Ruvkun, G .

NATURE, 2000, 408 (6808) :86-89

[32] CLUSTAL-W - IMPROVING THE SENSITIVITY OF PROGRESSIVE MULTIPLE SEQUENCE ALIGNMENT THROUGH SEQUENCE WEIGHTING, POSITION-SPECIFIC GAP PENALTIES AND WEIGHT MATRIX CHOICE [J].

THOMPSON, JD ;

HIGGINS, DG ;

GIBSON, TJ .

NUCLEIC ACIDS RESEARCH, 1994, 22 (22) :4673-4680

[33] Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets -: art. no. R65 [J].

Wang, XJ ;

Reyes, JL ;

Chua, NH ;

Gaasterland, T .

GENOME BIOLOGY, 2004, 5 (09)

[34] New human and mouse microRNA genes found by homology search [J].

Weber, MJ .

FEBS JOURNAL, 2005, 272 (01) :59-73

[35] Congruence and controversy: Toward a higher-level phylogeny of diptera [J].

Yeates, DK ;

Wiegmann, BM .

ANNUAL REVIEW OF ENTOMOLOGY, 1999, 44 :397-428

[36] OPTIMAL COMPUTER FOLDING OF LARGE RNA SEQUENCES USING THERMODYNAMICS AND AUXILIARY INFORMATION [J].

ZUKER, M ;

STIEGLER, P .

NUCLEIC ACIDS RESEARCH, 1981, 9 (01) :133-148

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