The sequence editor tool is an intuitive tool designed to efficiently edit and visualise genetic sequences within your workspace, including DNA sequences, plasmids and primers. Link your designs to your inventory and notebook entries or keep a shared library of molecular designs with colleagues. This article details the features of the sequence editor and explains how to get started with the sequence editor.
Features and functionality:
- Plasmid design - upload, edit, analyse and annotate all elements of your plasmids including primer binding sites.
- ORFs and protein translations - translate DNA sequences directly to amino acid sequences.
- Import and export sequences. Import *.gb, *.gbk *.fa files or export sequences as a Genebank, Fastq or Teselagen JSON file.
- Save DNA and AA sequence libraries - sequences can be used and referenced across all Labstep modules.
- Enzyme library - select enzymes from a standard library or add your own enzyme designs.
- Virtual digest - view enzyme cutsites and generate virtual digest details such as fragment length and overhang.
- Visual gel digest - visualise resulting size of DNA fragments in a virtual gel.
Accessing the Sequence Editor
To access the sequence editor tool:
1. Go to your experiment and add a data entry by clicking the “+” symbol. The sequence editor can be opened whenever you add a data element.
2. Choose “sequence” as data type
3. Name your sequence – this can be edited later.
4. Clicking “done” will take you to a genetic map window where you will be able to enter and edit your sequence.
Sequence can be created via importing *.gb, *.gbk, *.ape files. You can export and import sequences through the “file” tab at the top left corner of the window. To do so:
File -> Import sequence.
Sequences can be exported and downloaded onto your device in the following supported text-based formats:
- FASTA format: this format can be downloaded and opened with Jalview and Genome Compiler for both Mac OS X and Windows and can be copied directly into genome browsers such as Ensembl
- Genbank file: files of this type can be viewed using programmes such as SnapGene Viewer and Snapgene for Windows
Files of the aforementioned format can also be imported from your computer directly into your data entry space within the experiment. The genetic map will then be automatically recognized and opened.
Entering and Navigating Through Sequences
After you have created a sequence data entry point, you can:
- Directly copy and paste a sequence into the box on the right-hand side of the screen, or
- Enter a custom sequence manually
When the sequence has been entered, you will be able to view:
- Sequence map on the left-hand side of the screen
- Detailed features of the sequence on the right-hand side of the screen.
At the bottom of the page you will be able to change your sequence type from circular to linear and vice versa, which will be instantly mirrored on your genetic map. In the images below, you can find examples of circular (pUC18 plasmid) and linear (ACTN3 exon 1) DNA sequences.
Note: you can change the nature of the sequence from linear to circular at the mid-bottom of the screen as well as change the view of the genetic map from circular to linear. Make sure that both of these are the same to avoid confusion by viewing a circular sequence on a linear map and vice-versa.
When the sequence is entered, the following features that have been identified by the system will be automatically outlined:
- DNA cut sites
- Promoter regions
- Open reading frames are automatically outlined
- Primer regions
Using the tool ribbon will allow you to access some general features such as:
- Saving your sequence entry file
- Importing and exporting your sequence
- Undo/redo action
You will also find more quick-view tools such as:
- Show/hide and filter the cut sites
- Show/hide the primers
- Show/hide ORFs
- Save, import and export the sequence
On the right-hand side of the tool ribbon you will also find access buttons for some privacy settings such as visibility options and read-only mode.
Editing a Sequence
Add a plasmid editor widget and you can starting load sequence and see the features at the real time. All the feature will be loaded automatically and the sequence can be changed on the right side of the panel.
Accessing the “edit” tab allows you to create new elements for your sequence. Here you can add and sort more than 80 types of features and parts such as:
- 5’/3’ untranslated regions
- Attenuator sequences
- Conserved regions
These can be now named and will be mirrored on both your genetic map and the detailed sequence overview.
All features are summarized in the tab of Features. You have the option to change the color, name, type, strand. Select a sequence and right click to change / delete / create a feature. To reach this:
- Click the Properties on the right side panel
- Click Features
- Select a feature
- Click New to create a new feature
- Click Edit to edit the current selected feature
- Click Delete to remove a feature
Through the edit tab you can also translate your entire sequence. The translated sequence will be mirrored in the right-hand box and will now also include the corresponding amino acids (see image below).
The edit tab also allows you to create a new primer by simply introducing the start and end region for the primer.
The primer will now also be present on your genetic map as an arrow.
The “tools” tab allows users to virtually simulate an enzyme digestion using enzymes that match the DNA cut sites identified within the genetic sequence. To use this feature:
- Click the “tools” tab
- Simulate digestion
- You can simulate enzyme digestion by pressing COMMAND+D on Mac OS X or Ctrl+D on Windows directly from the main page
You can also add more enzymes into your digestion simulations using the built-in enzyme libraries, or, if the enzyme is not yet in the database, create a new enzyme by recognition sequence.
Managing enzyme cut sites
All cut sites will be listed under cut sites.
Running a virtual digest
The size of the DNA fragment can be viewed at the virtual digest.
Changing the Sequence View
Clicking the view tab will present you with a variety of customisable features which you can use to detail and personalise your sequence view. Given that you have added features, parts and primers to your sequence as demonstrated in previous steps, you will now be able to decide whether you would like these to be included on your genetic map. By ticking the specific characteristics in the “view” tab, you can control what appears on your map.
The view tab will allow you to:
- Show/hide features, translations, primers, parts, cut-sites and ORFs. If hidden, these will be not shown on both the circular/linear map and the sequence map
- Show/hide axis and axis numbers. This will remove the indicative axis and bp numbers from both the circular/linear map and the sequence map
- Show/hide amino acid numbers that indicate every 10th amino acid in the code. This can only be accessed after the sequence or a portion of a sequence has been translated and selected
- Show/hide reverse sequence, feature labels and colour code nucleotide bases
Use the widget (Files, File, Files (No Preview)) to display the map of a *.gb in circular or linear format. GenBank (*.gb) is a plaintext format for storing DNA data as character sequences. Read here for more details.
You can switch to read-only mode by either clicking the lock button at the right-hand side of the tool ribbon or alternatively enabling read-only mode through the “file” tab. Enabling this mode will disable your access to all editing features and secure your work until re-enabled.
Sequence can be exported from
File -> Export sequences. This supports:
- Genebank File
- Fastq file
- Teselagen JSON file