Working with DNA Sequences

How to register DNA sequences

Michael Fero PhD avatar
Written by Michael Fero PhD
Updated over a week ago

In TeselaGen’s BUILD module, a DNA sequence defines the DNA materials. We store each DNA sequence as a unique record in the ‘DNA Sequences’ database. In this tutorial, we will show you different ways a DNA sequence is registered in the database, explain what happens when a sequence is registered, and what can you do with a sequence in the database. 

1. Register DNA Sequences

You can register DNA sequences directly or indirectly by uploading sequence files and manually creating sequences or by importing a j5 assembly report that contains sequence information and registering plates containing DNA materials. 

1.1. Direct method: From the header, go to ‘Materials’ > ‘DNA Sequences’. This will take you to the ‘DNA Sequences’ library, which lists all unique DNA sequences registered in the app. 

1.1a. To create a new DNA sequence manually or upload sequence files in bulk, click on ‘Upload’ and select ‘DNA Sequences’. Follow the ‘Upload Sequences’ prompt to either ‘click or drag to upload’ sequence files. If you want to manually create a DNA sequence, Click ‘Paste Sequence’ (in upper right hand corner). Give the sequence a name (naming is optional but highly recommended), type or paste the sequence into the ‘Sequence’ field, select a DNA type from 4 available options (Linear DNA, Oligo, Plasmid and RNA). 

Figure 1: Creating DNA Sequence Manually

Click ‘Submit’ to register the DNA sequence to the ‘DNA Sequences’ library. This also automatically creates a DNA material record of this sequence in the ‘DNA Materials’ library.

1.1b. To upload DNA sequences in bulk, you can zip all the files (Genbank sequence format) into a compressed folder or multi-select the individual sequence files and drop the zip folder or the files into ‘Upload Sequences’, select the ‘DNA Material Type’ and click ‘Submit’. This will register the sequences in these files to the ‘DNA Sequences’ library and create corresponding DNA material records in the ‘DNA Materials’ library. If you want to tag the sequences being uploaded/created with specific labels, click ‘Add Tag’ to select pre-made tags or create a new tag. 

Figure 2: Uploading Sequence Files

If the uploaded sequence has regions annotated as features, these features will be parsed, collected and registered in the ‘Sequence Features’ library. Additionally, any features that are annotated as ‘CDS’ (coding sequence) in the sequence file will be pulled out as new sequences and registered as ‘CDS’ sequence type in the ‘DNA Sequences’ library, as well as the ‘Coding DNA Sequences’ library (a sub-library of the DNA Sequences library). Furthermore, an amino acid sequence record is created for each of the CDS sequences pulled from the uploaded sequence file, which is accessible through the ‘Amino Acid Sequences’ library. 

Figure 3: View of Sequence Features Library

Figure 4: View of Coding DNA Sequences Library

Figure 5: View of Amino Acid Sequences Library

1.2. Indirect methods: DNA sequences can also be registered by uploading plates containing DNA materials or importing j5 assembly reports (tutorial links to be added). Briefly, the j5 assembly report contains sequence information of the input parts, assembled pieces, primers, etc. Upon import of the j5 report, the sequence data associated with these parts are registered in the ‘DNA Sequences’ library. Similarly, when a plate containing DNA materials is uploaded, the sequence data (sequence files) associated with the DNA materials is also registered in the ‘DNA Sequences' library. 

2. Sequence’s attributes in DNA Sequences library view

Figure 6: View of DNA Sequences library

Name: The DNA sequence name is transferred with the sequence files (if uploaded) or user-created name (if manually created)

Size (bp): the number of base pairs in the DNA sequence and calculated from the sequence. 

Sequence Type: The sequence type information (eg. circular DNA) is captured from the sequence file. 

Features: this attribute is a list of all the features annotated in the DNA sequence. Each time a sequence with features is created, its features are also registered in the ‘Sequence Feature’ library (add documentation link)

Tags: list of all tags applied to the sequence (defined by users)

Lab Group: the lab group to which the sequence data belongs (defined by users)

Created By, Created, Modified: Captures any historical data regarding the sequence; i.e., user who creates the sequence, the time it was created and modified, respectively. 

Extended Properties: these are any custom attributes pre-defined by users (in App Settings). Users can apply or update the sequence’s extended properties in the sequence record view (double-click on a sequence or right-click it and select ‘View’). Once an extended property is applied to the sequence, it will be shown as a column in the library view.

3. View, update, export, and delete sequence records

3.1 View and update: To view a sequence, either double-click on the sequence or right-click and select ‘View’. This will take you to the sequence record view in which sequence information and a preview of the sequence are shown together with options to update or delete the sequence. You can update the sequence name, description, tags and extended properties. 

Figure 7: DNA sequence record view

To view the sequence and its features in the vector editor, hover over the preview image and click ‘Open Editor’. Note that this is a read-only vector editor. 

Figure 8: View of sequence in vector editor

3.2 Export: Within the vector editor, you can export a single sequence to Genbank, FASTA and JSON file formats. To export multiple sequences, from the library view select sequences for export, right-click and select ‘Export Genbank’. This will zip the Genbank files of the selected sequences into a compressed folder which you can download. 

3.3 Delete: To delete a single sequence record or multiple records from the library view, right-click on the selected record(s) and selecting ‘Delete’. 

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