How to create a new Biomodule from file

A biomodule is any linear double-stranded DNA fragment with a well defined biological function such as CDS, terminator, or gRNA. Here you will find how to create your biomodules and edit the basic information linked to them.

Access Biomodules area 

Log-in to Doulix and click on the hamburger button on the top left-hand side of the page. 

Select the Biomodules navigation item of the vertical menu on the left.

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Create a new Biomodule

To create a new Biomodule click on “CREATE NEW”. You'll be redirected to Doulix Biomodule Editor to create your own collection of DNA parts. 

 

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Upload your sequence 

The Biomodule Designer allows you to upload your DNA sequences in FASTA or GenBank format. Alternatively, you can type in your sequence and assign a name to your new Biomodule.

 

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Specify the biosafety level of the DNA sequence you intend to work on, tick the box declaring it has no dual use, and click on the “Proceed” button. 

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Edit information about your Biomodule

Once you clicked on “Proceed”, Doulix will automatically associate your Biomodule with:

  • a Part ID: a seven-character code identifying univocally your new Biomodule
  • a Sequence Name
For the sequence name, please note that:
  • If you uploaded your sequence in GenBank format, Doulix automatically will name it as the locus name reported in the gb.file.
  • If you uploaded your sequence in FASTA format, Doulix automatically will name it as reported in the first line of the corresponding FASTA file.
  • If you directly typed in your DNA sequence, your sequence name corresponds to the one you typed in.
To edit any information related to your Biomodule, click on Edit info and update the basic information.
 
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Here, there are many fields you can associate with your new Biomodule. Mandatory fields are indicated with an asterisk (*).

  • Sequence name*:  you can change the name of your Biomodule at your convenience.
  • Registry code: For iGEMers, if your DNA part has been registered in the iGEM Parts Registry, you can add your code (ex. BBa_X12345) in this field.
  • Suitable for: a checkbox list allows you to select the host organisms for your Biomodule.
  • Alternative name: if your sequence has an alternative name, you can report it here.
  • Description: A brief description of the function or composition of your DNA part.
  • Version: if you are working on several versions of the same sequence, you can associate a version name to each of them (we recommend to use only numbers 1 in compliance with the genebank standard syntax)
  • Division:  a drop-down menu lists some GenBank divisions. If your GenBank division is not on the menu, you can write to support at doulix dot com and we will be happy to add it in the next future.
  • Biosafety Level*: Doulix strictly follows the Harmonized Screening Protocol set by the International Gene Synthesis Consortium to promote biosecurity. Choose between Level 1 and Level 2.
  • Source organism: a drop-down menu lists the main source organisms. If your source organism is not on the list, chat with us or email us and we will be happy to add it.

 

Once you have finished editing, click on the “Update” button.

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Done 😀