psRNATarget

psRNATarget predicts plant small RNA (miRNA and ta-siRNA) target sites on transcripts by combining reverse complementary matching and target-site accessibility assessment to support analysis of gene expression regulatory networks.

Key Features:

• Supported small RNAs: Detects plant microRNAs (miRNAs) and ta-siRNAs, typically 20–24 nucleotides in length.
• Reverse complementary matching: Employs a scoring schema to perform reverse complementary matching between small RNAs and target transcripts.
• Target-site accessibility evaluation: Calculates unpaired energy (UPE) to assess the energy required to open the mRNA secondary structure surrounding target sites.
• Mechanistic inference: Uses accessibility and complementarity metrics to help distinguish translational versus post-transcriptional inhibition mechanisms.
• Interaction reporting: Reports potential small RNA/target site pairs and the number of interactions that could influence binding activity.
• Recognition rule integration: Incorporates recent findings in plant miRNA target recognition into prediction criteria.
• High-throughput computing: Implements a distributed computing back-end pipeline running on a Linux cluster for large-scale analyses.

Scientific Applications:

• GRN analysis: Identification of small RNA-mediated regulatory interactions within plant gene expression regulatory networks (GRNs).
• Target identification: Detection of miRNA and ta-siRNA targets among transcription factors and development-related genes.
• Mechanism discrimination: Differentiation between translational inhibition and post-transcriptional cleavage as regulatory outcomes.
• High-throughput prediction: Large-scale prediction of small RNA targets across transcriptomes.

Methodology:

Reverse complementary matching between small RNAs and transcripts using a scoring schema. Calculation of unpaired energy (UPE) to evaluate target-site accessibility in mRNA secondary structure. Execution on a distributed computing back-end pipeline running on a Linux cluster.