MTide

MTide identifies genome-wide plant microRNA (miRNA)–target interactions (MTIs) by analyzing small RNA and degradome sequencing data.

Key Features:

• Modified miRDeep2: A modified version of miRDeep2 is used to detect known and novel miRNAs from small RNA sequencing data and to accommodate plant-specific datasets.
• Adapted CleaveLand4: A modified CleaveLand4 algorithm analyzes degradome sequencing data to identify cleaved mRNA targets indicative of miRNA-mediated cleavage.
• Custom integration scripts: Supplementary custom scripts integrate miRNA and degradome results to systematically identify miRNA–mRNA pairs and reconstruct regulatory interaction networks.

Scientific Applications:

• Genome-wide miRNA target identification: Enables large-scale discovery of miRNA targets across plant genomes using small RNA and degradome sequencing.
• Post-transcriptional regulatory network reconstruction: Supports mapping of miRNA–mRNA interaction networks underlying gene expression regulation.
• Developmental biology studies: Facilitates investigation of miRNA roles in plant development through target identification.
• Stress response research: Enables identification of miRNA-mediated regulatory changes associated with abiotic and biotic stress responses in plants.

Methodology:

Small RNA sequencing data are analyzed with a refined miRDeep2 to identify known and novel miRNAs; degradome sequencing data are processed with an adapted CleaveLand4 to pinpoint mRNA cleavage sites; results are integrated via custom scripts to identify MTIs.