Software

Our software helps you design your own split ribozyme system to detect RNA or couple expression of two proteins.

Design your own detection system

Our SPEAR system is a new way to detect RNAs longer than 220 base pairs. Using split ribozymes SPEAR can not only be used to detect RNAs but couples the translation of a reporter or other protein to the transcription of a long RNA or mRNA. Besides detecting the presence of a specific RNA, SPEAR also allows the simple coupling of the expression of two proteins. This might be advantageous for iGEM Teams looking for innovative methods to regulate their synthetic circuits.

To facilitate the usage of the split ribozymes for other iGEM Teams we developed a software that automatically provides you the sequence of your whole split ribozyme which can be used to detect your target sequence.

As input the user only has to indicate the desired sequence for detection and the sequence of the reporter. Our software then designs guide RNA sequences and marks their corresponding binding sites in your target sequence. In a last step the software adds the biobrick suffix/prefix, promoters, RBS and terminators to the sequence which then can be synthesized.

Step-by-step-instruction:

  1. Go to our software gitlab

  2. Open the directory. Download all 4 files into one folder on your computer

  3. Go to that folder on your computer. Open the .exe file.

  4. You are told to put in your target sequence. That can be any sequence you want to detect whether it is coding or not. Copy your sequence into the command line and press enter. !Note: your sequence has to be longer than 220 base pairs.

  5. You are told to input your reporter sequence. Copy your reporter sequence starting with the start codon ATG and ending with a stop codon (TAG, TAA, TGA)

  6. If you entered your sequences correctly, the following will be shown to you:

    1. the binding sites of the guide RNAs in your target sequence

    2. the guide RNA sequences

    3. the complete sequence that you can get synthesized. This contains

      1. the biobrick suffix and prefix

      2. promoter Bba_J23115

      3. RBS Bba_K4472997

      4. split ribozyme half 1 (Bba_K4472999)

      5. your guide RNA 1

      6. T500 terminator

      7. promoter Bba_J23116

      8. split ribozyme half 2 (Bba_K4472998)

      9. your guide RNA 2

      10. your reporter

      11. T500 terminator

  7. If you made an error, the corresponding error message is shown and you have the chance to put in your sequence again.

Access Wiki Tools View Source Code