Dotplot plugin

UGENE Dotplot plugin provides a way to build dotplots and compare two biological sequences graphically. You can identify such elements as mutations, invertions, insertions, deletions, low-complexity regions.

Also the plugin provides advanced features sush as building and comparing multiple dotplots, dotplots navigation synchronization, saving and loading dotplots.

Usage example:

1. Activate „Tools > Build dotplot“ menu
   
   
   
   
   
   

2. Select the sequences to compare
   
   
   
   
   
   

3. Specify the dotplot parameters
   
   
   
   
   
   

4. Get the dotplot at the top of the created multiple sequence view
   
   
   
   
   
   

   Details
   

   Dotplot is a two-dimensional plot consisting of dots.

   Every dot on the plot corresponds to a matched base symbol at the dots „x“ position of the horizontal sequence and at the dots „y“ position of the vertical sequence.

   The „Minimum repeat length“ parameter of the dotplot parameters dialog allows to draw only such matches between the sequences that are continuous and long enough. Its value can be automatically arranged to an appropriate value by pressing the „1k“ results button.

   Visible diagonal lines indicate match between sequences in the given particular region.

   You might find helpful the Recognizable elements section of this document.
   
   

   Note: Dotplot plugin uses Repeat Finder plugin to build dotplot, make sure you have Repeat Finder plugin installed first.

   Navigation
   

   • Rotate mouse wheel or press the zoom buttons the left from a dotplot to zoom in and out.

   • Hold the middle mouse button and move the mouse cursor over the dotplot to move the zoomed region of the dotplot.

     or

   • Click on the desired region on the minimap.
     
     
     
     
     
     

   Selections
   

   Hold the left mouse button and drag the mouse cursor over a dotplot to select a dotplots region.

   To select a region corresponding to a particular repeat click near the repeat.
   
   

   
   
   
   

   The corresponding selections are also made on all the connected sequence views.
   The opposite is true as well, selecting a sequence region leads to creating a selection on a dotplot.

   Recognizable elements:
   
   
   

   
   
   
   
   1. Matches
   
   A match between sequences looks like a diagonal line representing continous match (or repeat).
   
   
   2. Frame shifts
   
   
   1. Mutations
   Mutations are distinctions between sequences represented by gaps in diagonal lines. They interrupt matches.
   
   
   2. Insertions
   Insertions are parts of one sequence that are missed in the another, while the surrounding parts match. In other words, an insertion is a subsequence that was inserted into a sequence.
   
   Graphically, insertions are represented by gaps which lie only on one axis. A little shift towards the other axis indicates a mutation involved.
   
   
   3. Deletions
   A deletion is a subsequence that was deleted from a sequence.
   A deletion from sequence A found in sequence B can be considered as an insertion into sequence B and contained in sequence A.
   
   
   3. Inverted repeats
   
   UGENE Dotplot plugin allows to search for inverted repeats as well. Inverted repeats are shown contrary to the direct repeats.
   
   Use the „Search direct repeats“ and „Search inverted repeats“ options of Dotplot parameters dialog to select which repeats to draw.
   
   It is possible to specify which colors to use for direct and inverted repeats by pressing the corresponding button.
   
   
   
   
   
   
   4. Low-complexity regions
   
   A low-complexity region is a region produced by redundancy in a particular part of the sequence. It is represented on a plot as a rectangular area filled with the matches.
   
   
   
   
   
   
   The corresponding parts of the comparing sequences will contain mostly one or a few base symbols.

   Tip: Compare sequence with itself to easily find low-complexity regions in it.

   Plugin features and tips:
   

   • Build a dotplot for currently opened sequences
   
   To build a dotplot for currently opened sequences, create a multiple view containing this sequences. It can be arranged by dragging the corresponding sequence objects (the items strated with the „[s]“) into the same sequence view.
   
   Then right-click on the created view and select „Analyse > Build dotplot“. Every sequence from the current multiple sequence view can be used to build the dotplot.

   Note: If you need to compare a sequence with itself, you can activate the menu from a single sequence view.

   
   
   
   
   
   
   
   • Compare several dotplots
   
   Dotplots created for the same view are shown at the same view.
   
   If the horiznotal and vertical sequences of several dotplots are the same correspondingly, it is possible to lock all zooming and navigating operations for these dotplots. Press the „Multiple view synchronization lock“ button the left of the dotplots.
   
   
   
   
   
   
   • Edit dotplots parameters
   
   It is possible to edit parameters of a built dotplot. Right-click on a dotplot and select „Dotplot > Parameters“. The parameters dialog will be re-opened.
   
   
   • Save dotplot as an image or in a native format. Load dotplots.
   
   To save a dotplot as an image, right-click on a dotplot and select „Dotplot > Save/Load > Save as image“.
   
   To save a dotplot in a native format, right-click on a dotplot and select „Dotplot > Save/Load > Save“.
   
   
   
   
   
   
   To load a dotplot, right-click on a dotplot and select „Dotplot > Save/Load > Save“. Then choose the desired .dtp-file. Its content will be loaded into the selected dotplot area.