Reliable prediction of Drosha processing sites improves microRNA gene prediction

被引:67
作者
Helvik, Snorre A.
Snove, Ola, Jr.
Saetrom, Pal [1 ]
机构
[1] Norwegian Univ Sci & Technol, Dept Comp & Informat Sci, NO-7052 Trondheim, Norway
[2] Interagon AS, Laboratoriesenteret, N-7006 Trondheim, Norway
[3] Norwegian Univ Sci & Technol, Fac Med, Dept Canc Res & Mol Med, NO-7489 Trondheim, Norway
关键词
D O I
10.1093/bioinformatics/btl570
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Mature microRNAs (miRNAs) are processed from long hairpin transcripts. Even though it is only the first of several steps, the initial Drosha processing defines the mature product and is characteristic for all miRNA genes. Methods that can separate between true and false processing sites are therefore essential to miRNA gene discovery. Results: We present a classifier that predicts 5' Drosha processing sites in hairpins that are candidate miRNAs. The classifier, called Microprocessor SVM, correctly predicts the processing site for 50% of known human 5' miRNAs, and 90% of its predictions are within two nucleotides of the true site. Another classifier that is trained on the output from the Microprocessor SVM outperforms existing methods for prediction of unconserved miRNAs. Reanalysis of characteristics and supporting evidence for a set of newly annotated miRNAs shows that some miRNAs may be misannotated. This suggests that expressed hairpins should not be annotated as miRNAs until they are verified to be Drosha and Dicer substrates.
引用
收藏
页码:142 / 149
页数:8
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