si-Fi

si-Fi designs RNAi target sequences and predicts off-target interactions to optimize specificity and efficiency in RNA interference experiments.

Key Features:

• Design Optimization: Designs RNAi sequences tailored to achieve effective knock-down of specified target genes.
• Efficiency Prediction: Predicts the silencing efficiency of candidate RNAi constructs to prioritize sequences with higher likelihood of successful gene knock-down.
• Off-Target Search: Identifies potential off-target interactions based on sequence complementarity to reduce unintended gene silencing.
• Custom Sequence Databases: Supports screening against custom sequence databases provided in FASTA format for organism-specific analyses.

Scientific Applications:

• Posttranscriptional Gene Silencing (PTGS): Supports design and assessment of RNAi constructs for studies of PTGS.
• Transcript Abundance Regulation: Enables experiments probing regulation of transcript abundance via targeted RNAi.
• Plant Antiviral Responses: Supports investigations into plant immune responses to viruses mediated by RNAi.
• Genomic Stability and Retroelements: Facilitates studies on genomic stability through silencing of retroelements.

Methodology:

Uses nucleic acid complementarity to optimize sequence design and to predict both silencing efficiency and off-target effects.