miRU

miRU predicts plant microRNA (miRNA) target sites by identifying complementary base-pairing interactions between mature miRNAs and plant mRNAs to support analysis of miRNA-mediated gene regulation.

Key Features:

• Input Flexibility: Accepts a mature miRNA sequence from any plant species as input.
• Comprehensive Search Capability: Conducts exhaustive searches for complementary target sites within large datasets of plant gene sequences.
• Mismatch Tolerance and Scoring: Accounts for mismatches in miRNA–target recognition and estimates likelihood of true versus false positives based on the number and type of mismatches.
• Evolutionary Conservation Analysis: Evaluates conservation of target complementarity across genomes guided by the conservation status of the miRNA.
• Output Content: Reports predicted target sites with complementarity alignments, original gene sequences, associated functional annotations, and ranking by mismatch score.

Scientific Applications:

• miRNA target identification for functional genomics: Predicts target genes to facilitate studies of plant miRNA functions and gene expression regulation.
• Investigation of molecular mechanisms and stress responses: Enables exploration of miRNA-mediated mechanisms underlying biological processes and stress responses in plants.
• Comparative genomics of miRNA targets: Supports analysis of conservation of target sites across plant genomes.

Methodology:

Computational sequence similarity searches tailored to plant miRNA–mRNA near-perfect base pairing, incorporating mismatch-tolerant scoring and evolutionary conservation analysis.