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Chunxiao edited this page Jun 8, 2026 · 2 revisions

SeqImprove Tutorial

This session is about using SeqImprove to annotate the 4 plasmids from sc2 circuit

Step 1: Preparing data

Set up the foundation before starting work.

  • Download the PDF, read and understand the cs2 circuit design.
  • Download the 4 *.fasta file from link

Step 2: Using SeqImprove from SynBioSuite

  • Go to SynBioSuite: https://synbiosuite.org/
  • click “Use my local file system” -> Open Folder -> create a folder -> Select Folder
  • click Build -> import a plasmid. You should see SeqImprove
  • click From Scratch -> Submit
    1. In the OverView tab -> click the “pencil” button to set the DisplayId and Name of this plasmid to the same of the plasmid fasta filename. For example: DisplayId: plJAI478 -> click the check mark to save
    • Role: Engineered Plasmid (SO:0000637)
    • DNA Topology: Circular
    • Target Organisms: type E.coli, then it will show Escherichia coli
    • References: 10.1038/s41589-024-01730-1 (DOI https://doi.org/10.1038/s41589-024-01730-1 ), click +
    1. Go to Sequence Tab
  • use any text editor to open one of the fasta files, copy the DNA sequence only
  • click the pencil button on the Sequence text box
  • double click the space under “Enter some text…”
  • paste the sequence -> click the green check mark to save
    1. Annotate
  • In Algorithm: select FlashText -> leave all the check box empty
  • click Import Library: Login: Online database: https://synbiohub.org/, Email, passward -> submit
  • Select the Collection you curated from previous session -> submit -> you should see the collection name and a check box
  • select the check box of the collection -> click Analyze Sequence -> you should see colored parts
  • go to the Text tab, add description.
    1. Click Save to Working Directory
  • double click the saved plasmid, you should see the SBOL Visual Glyphs -> click some Engineered Region to explore, use the right and left arrow to go back or forward.
    1. Click the drop down right of “Save to Working Dir”, click “Upload to SynBioHub”, Use Existing Collection, -> Root Collection -> Select your “Build” Collection -> Submit.
    1. Go to SBH, and open the “build” collection, go to Members -> filter by “sbol2:ComponentDefinition”-> explore; filter by “engineered plasmid” -> open it, should be circular.
    1. Repeat these steps for the other 3 plasmids.

Step 3: Review (Optional)

  • Compare results against the original design
  • Why this is different from the original design
    • What worked well?
    • What could be improved?
    • Is there a bug of the software?
    • is the library not complete?
  • Archive final deliverables and close out the project
  • Explore different algorithms with different parameters
  • Do you find more annotations? Why?
  • Which algorithm works better on this example? Evaluate the outcome and capture lessons learned.

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