miRWoods

miRWoods is a software tool that identifies and annotates microRNAs (miRNAs) in eukaryotic genomes. It addresses the challenges of identifying valid miRNAs with low read counts, accurately locating hairpin precursors, and balancing precision and recall in miRNA prediction.

Key features of miRWoods include:

1. A duplex-focused precursor detection method
2. Stacked random forests with specialized layers to detect mature and precursor miRNAs
3. Optimization of the harmonic mean of precision and recall

Topic

Functional, regulatory and non-coding RNA;Gene transcripts;RNA-Seq;Model organisms

Detail

  • Operation: Sequence trimming;miRNA target prediction;miRNA expression analysis;Genome annotation

  • Software interface: Command-line interface

  • Language: Perl

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: Oregon State University, OSHU MRF, NIH.

  • Input: -

  • Output: -

  • Contact: David Hendrix david.hendrix@oregonstate.edu

  • Collection: -

  • Maturity: -

Publications

  • miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs.
  • Bell J, et al. miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs. miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs. 2019; 15:e1007309. doi: 10.1371/journal.pcbi.1007309
  • https://doi.org/10.1371/JOURNAL.PCBI.1007309
  • PMID: 31596843
  • PMC: PMC6785219

Download and documentation

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