miRdentify

miRdentify identifies microRNAs (miRNAs) with high stringency from animal high-throughput sequencing data to reduce false positives associated with increased read depth.

Key Features:

• Stringent Identification Process: Applies a transparent pipeline with more stringent criteria than many existing algorithms to reduce false positives while retaining sensitivity to novel miRNAs.
• Structural Recognition: Uses the structural definition of miRNAs—hairpin-loop precursors processed by Drosha and Dicer—to recognize precursors and mature ∼22-nucleotide miRNA guide strands.
• Broad Applicability Across Species: Identifies novel miRNAs across animal species, including human, mouse, Drosophila (fruit fly), and nematodes.
• Validation of Predictions: Predictions have been experimentally validated, including the identification and validation of over 400 novel human miRNAs and a reported male-specific miRNA.

Scientific Applications:

• Novel miRNA discovery: Discovery of novel miRNAs from animal sequencing datasets.
• miRNA characterization and gene regulation: Characterization of miRNA sequences and their roles in gene regulation.
• Developmental biology: Investigation of miRNA functions in developmental processes.
• Disease pathology: Investigation of miRNA involvement in disease and pathology.
• Evolutionary studies: Comparative and evolutionary analyses of miRNA repertoires across species.

Methodology:

miRdentify employs a transparent computational pipeline that applies stringent identification criteria and structural (hairpin) recognition of Drosha- and Dicer-processed precursors to identify mature ∼22-nucleotide miRNA guide strands.