Jemboss & Artemis - Circular Plot
Keywords: java, biology, bioinformatics, EMBOSS, Jemboss, Artemis

# DNA Circular Plot

This is a collaborative project between Jemboss and Artemis. It makes use of the existing circular plot in Jemboss and the Artemis sequence libraries.

It can be used to generate images of circular DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3.

The circular plots are interactive. The sections below describe how the circular plot can be altered and enhanced to arrive at the best view.

## Editing Features

Each feature drawn can be double clicked on to open up a properties window. This allows the label, start and end coordinates, colour and line width to be changed. There is also an option to show or hide the label.

## Dragging Features in a Track

Features can be dragged by selecting a feature and holding the mouse button down then dragging towards or away from the circular plot center. This alters all the features in that track, moving them towards or away from the center.

## Defining Tracks

Tracks of features of different radii can be set up. The features included in a track can be defined using the "Track Manager". Features can then be filtered to define what types of features are displayed on a given track. The feature key (e.g. CDS) and a qualifier can be used along with which strand (forward or reverse) the feature is on. The qualifier value can be a single value or a list of values. For example, if the qualifier "gene" is used with the values "a b c", then those three genes will be displayed on the track. Selecting 'Not' means that it will pick out everyting for a track except that qualifier.

The size of the track can be defined in the track manager. Also the position of the track can be set as a fraction of the radii. This is an alternative to dragging the features in a track to a different position. Features can be either coloured based on the colour qualifier or given all given the same colour within that track.

## Graphs

The %GC and GC skew ((G-C)/(G+C)) can be displayed. There is an options menu for eah plot to define the step size and window size for the calculation. The colours above and below the average for the plot can be selected to highlight the different regions. A user defined plot can be read in, this takes the same form as a single user plot in Artemis. This will prompt the user for the name of a data file which should contain one line per base of sequence and one floating point number per line.

## Ticks

Major and minor ticks can be adjusted from the 'Tick Marks...' menu. An interval for each of these can be set. Numbering for the ticks can optionally be turned off.

## Read in Entry on Separate Track

As with Artemis, it is possible to overlay features from a separate file. From the 'File' menu there is an option to 'Read in Entry on Separate Track'. This creates an extra track and adds all the features to the track.