Search for Inverted Repeats

For each input sequence, the workflow performs a search for inverted repeats.

It then saves the repeats found on the direct strand to the “direct_strand_repeat_units.fa” file and the complementary ones to the “compl_strand_repeat_units.fa” file.

How to Use This Sample

If you haven’t used the workflow samples in UGENE before, please look at the “How to Use Sample Workflows” section of the documentation.

Workflow Sample Location

The workflow sample “Search for Inverted Repeats” can be found in the “Scenarios” section of the Workflow Designer samples.

Workflow Image

The opened workflow looks as follows:

Workflow Wizard

The wizard has 3 pages.

1. Input sequence(s): On this page, you must input sequence(s).

   

2. Search for inverted repeats parameters: On this page, you can modify inverted repeats parameters.

   

   The following parameters are available:

   • Annotate as: Name of the result annotations marking found repeats.
   • Min length: Minimum length of repeats.
   • Identity: Repeats identity.
   • Min distance: Minimum distance between repeats.
   • Max distance: Maximum distance between repeats.
   • Filter algorithm: Filter repeats algorithm.
   • Algorithm: Control over variations of the algorithm.
   • Parallel threads: Number of parallel threads used for the task.

3. Output Sequences: On this page, you can modify result file(s) settings.