Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data.

ABSTRACT:

Background

Several methods exist for the prediction of precursor miRNAs (pre-miRNAs) in genomic or sRNA-seq (small RNA sequences) data produced by NGS (Next Generation Sequencing). One key information used for this task is the characteristic hairpin structure adopted by pre-miRNAs, that in general are identified using RNA folders whose complexity is cubic in the size of the input. The vast majority of pre-miRNA predictors then rely on further information learned from previously validated miRNAs from the same or a closely related genome for the final prediction of new miRNAs. With this paper, we wished to address three main issues. The first was methodological and aimed at obtaining a more time-efficient predictor, however without losing in accuracy which represented a second issue.

SUBMITTER: Higashi S 

PROVIDER: S-EPMC4448272 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature