Repeat Finder plugin

Repeat Finder plugin provides a tool to search for direct and invert repeats in a DNA sequence.

Usage example:

Open a DNA sequence in Sequence view and use "Analyse->Find Repeats" item in popup menu:

The repeats found are saved and displayed as annotations to the DNA sequence

Tandem repeats

To find tandem repeats, right click at the DNA sequence view and select the “Analyze->Find tandems” context menu item:

• Tandem preset
  Specify the tandem repeats parameters with pre-defined values by selecting the available preset:
  
  
  
• Min period, Max period
  The minimum and maximum acceptable repeat length measured in base symbols

• Algorithm
  The algorithm parameter allows to select the search algorithm. The default and a fast one is optimized suffix array algorithm.

• Minimum tandem size
  Minimum tandem size sets the limit on minimum acceptable length of the tandem, i.e. the minimum total repeats length of the sought-for tandem.

• Minimum repeat count
  The minimum number of repeats of a sought-for tandem

• Show overlapped tandems
  Check if the plugin should search for the overlapped tandems, otherwise keep unchecked

Specify the region to search in: the whole sequence, a custom region or the region of the current selection (if any).

Save annotation(s) to

Specify the existing or new annotations table file to save the resulting annotations into.

Annotation parameters

You can change the default group name and annotation(s) name values of the resulting annotation(s).

An example of the search results for the micro-sattellite preset:

Note: tandem repeats be interpreted as several tandem repeats with the least period and offset lesser than this period, merged into one case.