siRNA Design & Off-Target Profiling Platform

An automated, genome-wide specific siRNA design and off-target profiling pipeline optimized for T7 in vitro transcription (IVT).

🌟 Key Features

• Efficacy Guaranteed: Applies strict thermodynamic guidelines for highly effective siRNA selection.
• High Specificity: Prevents seed-dependent off-target effects by strictly evaluating the melting temperature (Tm ≤ 21.5°C) of the seed region using the Nearest-Neighbor method.
• Genome-wide Profiling: Automates BLAST+ searches against mammalian genomes (via Google Drive or NCBI Datasets) to rigorously filter out potential off-targets.
• Common Target Mode: Capable of identifying conserved siRNA sequences across multiple gene variants or species.
• Ready for IVT Synthesis: Automatically generates order-ready DNA template sequences with customizable T7 promoters and 5' extensions.
• Zero Environment Setup: Fully executable in the browser via Google Colab.

🚀 Pipeline Overview

This tool guides you through 5 simple steps:

1. Target Discovery: Input your sequence (single or multiple) to find candidates meeting the design criteria.
2. Genome Database Setup: Mount your custom genome (.fna) or download directly from NCBI.
3. Off-target Profiling: Strict screening using blastn-short to evaluate off-target risks.
4. Template Generation: Output clean, order-ready CSV files for DNA oligo synthesis.

📖 Citations & Algorithms

This pipeline evaluates siRNA candidates based on the established thermodynamic rules:

• Efficacy: Ui-Tei, K. et al., Nucleic Acids Res 32, 936-948 (2004).
• Specificity: Ui-Tei, K. et al., Nucleic Acids Res 36, 7100-7109 (2008).

👤 Author

Fumiya Hasegawa, DVM

⚠️ Disclaimer

This software is provided for academic and research purposes only. The author assumes no responsibility or liability for any errors, omissions, or any direct, indirect, or consequential damages arising from the use of this tool or the information generated by it. Use at your own risk.