SoMART

SoMART identifies and analyzes microRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs), their precursors, degradome signatures, and target sites to support analysis of sRNA-mediated gene regulation.

Key Features:

• Slicer Detector: Detects small RNAs (sRNAs) that target specific input genes to identify potential regulatory cleavage events.
• dRNA Mapper: Detects degradome RNA products derived from input genes using a dRNA-seq protocol that generates longer reads to enhance characterization of miRNA precursors.
• PreMIR Detector: Identifies miRNA precursors (MIRs) and tasiRNA precursors (TASs) based on input sRNAs.
• sRNA Mapper: Maps sRNAs onto input genes to locate sRNA–genomic interactions and candidate target sites.

Scientific Applications:

• Plant species datasets: Includes sRNA, dRNA, and genomic DNA or transcriptome data from Arabidopsis and solanaceous plants such as potato (Solanum tuberosum) and tomato (Solanum lycopersicum).
• miR172–APETALA2 characterization: Used to characterize miR172-mediated regulation of the APETALA2 gene in potato.
• MIR390–TAS3 conservation: Confirmed conservation of MIR390-triggered TAS3 in tomato (Solanum lycopersicum).
• MIR482–TAS5 prediction: Predicted the existence of MIR482-triggered TAS5 in tomato.
• Validation in Arabidopsis: Validated using analyses of 21 confirmed miRNA targets and 115 miRNA precursors in Arabidopsis thaliana.

Methodology:

Combines bioinformatics prediction with processing of dRNA-seq-derived degradome reads to identify miRNAs, tasiRNAs, their precursors (MIRs/TASs) and targets.