pssRNAit

pssRNAit designs siRNAs using integrated plant transcript datasets and computational models to enable specific gene silencing in plants.

Key Features:

• Integrated Transcript Dataset: Comprehensive transcript coverage from more than 160 plant species for target selection.
• Computational Models and Rules: Simulates the RNAi pathway with gene silencing rules to prioritize siRNA specificity and efficacy.
• Genome-wide Off-Target Assessment: Evaluates potential unintended interactions of designed siRNAs across homologous regions in plant genomes.
• siRNA Pool Design: Produces siRNA pools intended for expression via virus-induced gene silencing (VIGS) or synthetic vectors.

Scientific Applications:

• Functional Genomics Studies: Facilitates targeted gene silencing for studying gene function and trait improvement in plants.
• Experimental Expression and Validation: Supports generation of siRNA pools for VIGS or synthetic vectors with validation by reverse transcription quantitative PCR (RT-qPCR) and RNA-sequencing-based transcriptome analysis.

Methodology:

Designs siRNAs from an integrated plant transcript dataset (>160 species), applies computational models simulating the RNAi pathway with gene silencing rules, and performs genome-wide off-target assessment.