Get Your Desired Plasmid Copy Number

Using our tool, you can achieve a diverse range of plasmid copy numbers tailored to meet your exact requirements.

Instructions

How to use the Ctrl-C tool?

  1. Choose between (1) using the provided plasmids (currently supporting pUC-19 and pBR322), (2) uploading your own plasmid's FASTA file or (3) providing the plasmid's sequence as text.

    select-plasmidselect-fastaselect-sequence
    Figure 1:The tool supported inputs,from left to right- (1) Working with pUC19 or pBR322 plasmids. (2) Working with your own Fasta file. (3) Working with your own seqence, provided as text.

  2. Choose your desired copy number. If you want a grid (range) of copy numbers, first click on the “grid” option, then enter 5 values of your desired grid of copy numbers.

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    Figure 2 :From left to right- Copy number input box for a single output. Grid copy number input box for multiple output.

  3. Choose whether to visualize the annotated plasmid map or not.

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    Figure 3:Plasmid map visualization activation and deactivation button.

  4. Click “Get Modified Plasmid” and wait for the results to appear on the screen.

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    Figure 4:The sofrware "Run" button, while the modification are being made, the loading page (right) will apear.

  5. If “visualize the plasmid map” checkbox was marked, clicking on the different site of the plasmid's map illustration will refer the user to the site sequence.

    ewsult
    Figure 5:The intercative visualizations created by the software.

  6. Click “Download Modified Sequence” to download the plasmid modified sequence as a FASTA file.

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    Figure 6: Download buttun, the modifeid sequence will be saved to your comuter as a Fasta file.


What Ctrl-C tool does?

  • Given the input sequence, the tool annotates the sequence using DIAMOND.
  • After identifying the ORI’s (origin of replication) location, our tool modifies the plasmid's ORI sequence.
  • The ORI’s modified sequence affects the plasmids replication system, controlling the
  • The sequence is determined using our computational predictive model of the replication system of ColE1 plasmids.
  • If you choose to visualize the plasmid, DIAMOND Blast will add annotations for the modified plasmid sequence.


Typical Ctrl-C tool applications

Controlling the Copy Number had a wide range of applications:

  • Any project that involves working with plasmids, can benefit from controlling the plasmid Copy Number.
  • It offers an additional way to optimize and control recombinant protein expression.
  • Biosensors are innovative devices that detect and convert biological or chemical signals into measurable data. Adjusting plasmid copy numbers can help optimize the signal-to-noise ratio of biosensors.
  • Pathways containing multiple steps often require synchronization and optimization to avoid bottlenecks in the production of the final product. Controlling copy number was shown to be essential in such processes, to get better production and avoid cell toxicity.
  • Plasmid DNA vaccines represent an innovative vaccination approach, utilizing plasmids as both a carrier for antigens and a scalable means for vaccine production. Controlling plasmid copy number can help the production process.


FAQ

  1. Why do I get an Error "the promoter of the RNA-p sequence does not match the original promoter"?

    Our tool supports Col-E1 like plasmids only, that contains the wild type RNAp promoter sequence. Please make sure that the plasmid you are using contains the correct RNAp promoter.

  2. How accurate is the modification made by the Ctrl-C tool to the plasmid's ORI sequence?

    Our model reached high performance, with Pearson correlation of 0.96 and p-value of 7.92*10-70.

  3. Can I cite or reference the Ctrl-C tool in my research or publications?

    Yes. We plan to submit a paper about the tool. In the meantime, you can cite our website.

  4. Is the Ctrl-C tool compatible with all plasmid sequences?

    Our tool currently supports col-E like plasmids only.

  5. What are the system requirements for running the Ctrl-C tool?

    None! internet access only.

  6. What if I don’t know which plasmid to use?

    First, you can simply choose one of the default and recommended plasmids under ‘Selected Plasmids’. Second, you can enter any col-E plasmid you find into the tool and run with plasmid map visualization to get the annotations of the plasmid, which will show you what the plasmid contains.

  7. How to choose the desired plasmid copy number?

    If you don’t know which plasmid copy number is optimal for your need, no worries. By selecting ‘Grid’ in the desired plasmid copy number section, you will get the option to request a range of 5 different copy numbers, that can then be use to find the optimal copy number for you.

  8. Can I input multiple plasmids at once?

    Unfortunately, right now we only support one plasmid at a time, but hey, you can run it as many times as your heart desires.

  9. Can I integrate this tool as part of my own project?

    Yes, we have a public API available. For more information please visit the API documentation at this link


Under The hood

Ctrl-C tools make use of multiple advanced biosynthetic tools. First we use seqparse[5] for reading the plasmid input from the uploaded fasta file. Then we find the plasmid annotations with First we use pLannotate[4], a python library for automatically annotating engineered plasmids. Finally in order to visualize the beautiful annotated plasmid map, we use seqviz[2], an amazing javascript library that serves as a DNA, RNA, and protein sequence viewer.