sRNATargetDigger

sRNATargetDigger identifies sRNA-target gene pairs and co-regulatory relationships using high-throughput sequencing (HTS) and degradome sequencing data to map miRNA, ta-siRNA, and siRNA regulatory networks in plants.

Key Features:

• Bidirectional Identification: Two modules, Forward Digger and Reverse Digger, identify sRNA-target pairs starting from known sRNAs or from known target genes.
• Co-regulatory Network Analysis: Detects unknown sRNAs that co-regulate the same target gene, enabling identification of multi-sRNA co-regulation.
• Integration with Sequencing Data: Leverages high-throughput sequencing (HTS) and degradome sequencing data for large-scale mining of sRNA-target pairs.

Scientific Applications:

• Plant regulatory network mapping: Identification of known and novel sRNA-target interactions to study sRNA-mediated control of development, metabolism, and disease resistance in plants.

Methodology:

Computational pipeline uses two modules (Forward Digger and Reverse Digger) to integrate high-throughput sequencing (HTS) and degradome sequencing data for sRNA-target pair identification and co-regulatory relationship detection, and was validated by re-examination of published sRNA-target pairs in Arabidopsis thaliana where 170 novel co-regulatory pairs were identified.