title: MiRAuto: an automated user-friendly microRNA prediction tool utilizing plant small RNA sequencing data.
abstract: MicroRNAs (miRNAs) are a class of small RNAs that post-transcriptionally regulate gene expression in animals and plants. The recent rapid advancement in miRNA biology, including high-throughput sequencing of small RNA libraries, inspired the development of a bioinformatics software, miRAuto, which predicts putative miRNAs in model plant genomes computationally. Furthermore, miRAuto enables users to identify miRNAs in non-model plant species whose genomes have yet to be fully sequenced. miRAuto analyzes the expression of the 5'-end position of mapped small RNAs in reference sequences to prevent the possibility of mRNA fragments being included as candidate miRNAs. We validated the utility of miRAuto on a small RNA dataset, and the results were compared to other publicly available miRNA prediction programs. In conclusion, miRAuto is a fully automated user-friendly tool for predicting miRNAs from small RNA sequencing data in both model and non-model plant species. miRAuto is available at http://nature.snu.ac.kr/software/miRAuto.htm.
authors.affiliation: National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Jeongsoo
authors.initials: J
authors.lastname: Lee
authors.forename: Dong-In
authors.initials: DI
authors.lastname: Kim
authors.forename: June Hyun
authors.initials: JH
authors.lastname: Park
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.forename: Chanseok
authors.initials: C
authors.lastname: Shin
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D015723:Gene Library; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant