ViralmiR: A support-vector-machine-based method for predicting viral microRNA precursors

Kai Yao Huang, Tzong Yi Lee, Yu Chuan Teng, Tzu Hao Chang

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: microRNAs (miRNAs) play a vital role in development, oncogenesis, and apoptosis by binding to mRNAs to regulate the posttranscriptional level of coding genes in mammals, plants, and insects. Recent studies have demonstrated that the expression of viral miRNAs is associated with the ability of the virus to infect a host. Identifying potential viral miRNAs from experimental sequence data is valuable for deciphering virus-host interactions. Thus far, a specific predictive model for viral miRNA identification has yet to be developed. Methods and results: Here, we present ViralmiR for identifying viral miRNA precursors on the basis of sequencing and structural information. We collected 263 experimentally validated miRNA precursors (pre-miRNAs) from 26 virus species and generated sequencing fragments from virus and human genomes as the negative dataset. Support vector machine and random forest models were established using 54 features from RNA sequences and secondary structural information. The results show that ViralmiR achieved a balanced accuracy higher than 83%, which is superior to that of previously developed tools for identifying pre-miRNAs. Conclusions: The easy-to-use ViralmiR web interface has been provided as a helpful resource for researchers to use in analyzing and deciphering virus-host interactions.

Original languageEnglish
Article numberS9
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
Publication statusPublished - Jan 21 2015

Fingerprint

MicroRNA
MicroRNAs
Viruses
Precursor
Support vector machines
Support Vector Machine
Virus
Genes
Mammals
Sequencing
Cell death
RNA
Identification (control systems)
Apoptosis
Random Forest
Predictive Model
Human Genome
Interaction
Messenger RNA
Insects

ASJC Scopus subject areas

  • Applied Mathematics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

ViralmiR : A support-vector-machine-based method for predicting viral microRNA precursors. / Huang, Kai Yao; Lee, Tzong Yi; Teng, Yu Chuan; Chang, Tzu Hao.

In: BMC Bioinformatics, Vol. 16, No. 1, S9, 21.01.2015.

Research output: Contribution to journalArticle

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