title: Benchmark comparison of ab initio microRNA  identification methods and software.
abstract: MicroRNAs  (miRNAs) are short, non-coding RNA molecules that play an important role in the  world of genes, especially in regulating the gene expression of target  messenger RNAs through cleavage or translational repression of messenger RNA. Ab  initio methods have become popular in computational miRNA detection. Most  software tools are designed to distinguish miRNA precursors from  pseudo-hairpins, but a few can mine miRNA from genome or expressed sequence tag  sequences. We prepared novel testing datasets to measure and compare the  performance of various software tools. Furthermore, we summarized the miRNA  mining methods that study next-generation sequencing data for bioinformatics  researchers who are analyzing these data. Because secondary structure is an  important feature in the identification of miRNA, we analyzed the influence of  various secondary structure prediction software tools on miRNA identification.  MiPred was the most effective for classifying real-/pseudo-pre-miRNA sequences,  and miRAbela performed relatively better for mining miRNA precursors from  genome or expressed sequence tag sequences. RNA-fold performed better than  m-fold for extracting secondary structure features of miRNA precursors.
authors.affiliation: School of Information Science and Technology, Xiamen University, Xiamen, Fujian, China.
authors.forename: L L
authors.initials: LL
authors.lastname: Hu
authors.forename: Y
authors.initials: Y
authors.lastname: Huang
authors.forename: Q C
authors.initials: QC
authors.lastname: Wang
authors.forename: Q
authors.initials: Q
authors.lastname: Zou
authors.forename: Y
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D019985:Benchmarking; D003198:Computer Simulation; D057225:Data Mining; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D055029:Inverted Repeat Sequences; D035683:MicroRNAs / Q000235:genetics*; D009690:Nucleic Acid Conformation; D017423:Sequence Analysis, RNA; D012984:Software; D060388:Support Vector Machine
chemical_list: D035683:MicroRNAs