miRAuto: An automated user-friendly MicroRNA prediction tool utilizing plant small RNA sequencing data

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.

Researchers at Seoul National University 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

Availability – miRAuto is available at http://nature.snu.ac.kr/software/miRAuto.htm .

  • Lee J, Kim DI, Park JH, Choi IY, Shin C. (2013) miRAuto: An automated user-friendly MicroRNA prediction tool utilizing plant small RNA sequencing data. Mol Cells 35(4), 342-7. [abstract]