Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
<html>
<head>
<meta name="keywords" content="java, biology, bioinformatics, EMBOSS, Jemboss, Artemis">
<title>Jemboss & Artemis - Circular Plot</title>
</head>
<body text="#000000" bgcolor="#FFFFFF" link="#0000EE" vlink="#551A8B" alink="#FF0000">
<h1>DNA Circular Plot</h1>
This is a collaborative project between <a href="http://sf.net/projects/emboss">Jemboss</a> and
<a href="http://www.sanger.ac.uk/Software/Artemis">Artemis</a>. It makes use
of the existing circular plot in Jemboss and the Artemis sequence libraries.
<p>
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.
</p>
<p>
The circular plots are interactive. The sections below describe how the
circular plot can be altered and enhanced to arrive at the best view.
</p>
<h2>Editing Features</h2>
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.
<h2>Dragging Features in a Track</h2>
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.
<h2>Defining Tracks</h2>
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.
<p>
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.
</p>
<h2>Graphs</h2>
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.
<h2>Ticks</h2>
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.
<h2>Read in Entry on Separate Track</h2>
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.