HomeCLC FAQ - Analyses-related questionsSequences and sequence listsHow do I mark a sequence as circular or linear?

2.1. How do I mark a sequence as circular or linear?

Sequences have an attribute that marks them as circular or linear. If this feature is defined in the original GenBank file imported into the Workbench, the information is retained. This information will be shown when you open your sequence in text view (see the screen shot below).

If this attribute is not part of the sequence metadata on import, then the sequence will be considered as linear.


A single sequence can be marked as circular or linear either from the sequence or table view. More or all sequences in a sequence list can be marked as circular or linear at the same time from the table view. The following paragraphs describe the different options:

 

Marking sequence as circular or linear from the table view

If you have a list of sequences for which you wish to mark one or all sequences as circular or linear, then it can be done in the following way:

  • Open up your sequence list in table view
  • Select the row with the sequence to mark as circular. To mark all rows of the table by clicking a single row, then press Ctrl+A or ⌘+A on Mac
  • Move the mouse cursor over the column called Linear
  • Depress the mouse button and choose the option called Edit Linear
  • Choose the option from the menu that will appear:
    • Update linear to Circular or Linear

 

  • Click the Update button
  • Save the edits to the sequence list by clicking Save button in the toolbar or by using the keyboard shortcut Ctrl+S or ⌘+S on Mac

 

Marking sequences as circular or linear from the sequence view

If you have a single sequence object or an individual sequence in a sequence list, that you wish to mark as circular or linear, then it can be done in the following way:

  • Open your sequence or sequence list in a graphical view
  • Move the mouse cursor over the name of the sequence you would like to change from linear to circular or vice versa
  • Depress the mouse button and choose the option from the menu that will appear:
    • Make Sequence Circular or Make Sequence Linear

  • Save the edits to the sequence list by clicking Save button in the toolbar or by using the keyboard shortcut Ctrl+S or ⌘+S on Mac

 

 

What to do if I have a sequence track?

Only stand-alone sequence can be marked as circular or linear. Hence, to mark the mitochondrial chromosome as circular in a genome sequence track, please convert to a stand-alone sequence or sequence list, follow the steps outlined above, and then convert the final objects back to track format. Conversions to and from tracks can be done using the tools in the Genomics Workbench under:

Toolbox | Track Tools | Track Conversion

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