TAPIR

TAPIR predicts plant microRNA (miRNA) targets, including canonical targets and target mimics, to enable analysis of miRNA-mediated gene regulation in plants.

Key Features:

• Fast Algorithm: Rapid prediction mode that identifies potential miRNA targets using standard pairing criteria for large-scale analyses.
• Precise Algorithm: Comprehensive prediction mode that detects miRNA-target interactions with less-than-perfect base pairing, including target mimics characterized by large loops in the miRNA-target duplex.
• Target Mimic Detection: Explicit identification of target mimics formed by large loops in the miRNA-target duplex.
• Dual-option Approach: Provides a choice between computational efficiency and depth of analysis via two algorithmic modes.

Scientific Applications:

• Plant molecular biology: Prediction of miRNA targets to study miRNA-mediated regulation in plants.
• Genetics and developmental biology: Identification of targets and target mimics relevant to developmental processes regulated by miRNAs.
• Gene expression and stress response studies: Analysis of miRNA involvement in gene expression modulation and plant stress responses.

Methodology:

Analyzes miRNA-target duplexes using two algorithmic modes: a fast mode applying standard pairing criteria and a precise mode detecting less-than-perfect base pairing and large-loop target mimics.