The gap4 Contig Editor is designed to allow rapid checking and editing of characters in assembled readings. Very large savings in time can be achieved by its sophisticated problem finding procedures which automatically direct the user only to the bases that require attention. The following is a selection of screenshots to give an overview of its use.
The figure above shows a screendump from the Contig Editor
which contains segments of aligned
readings, their consensus and a six phase translation. The Commands menu
is also shown. The main components are: the controls at
the top; reading names on the left; sequences to their right; and status lines
at the bottom. Some of the reading names are written in light grey which
indicates that their traces/chromatograms are being displayed (in
another window, see below).
One reading name is written with inverse colours, which indicates that it
has been selected by the user. To the left of each reading name is the reading
number, which is negative for readings which have been reversed and complemented.
The first of the status lines, labelled "Strands", is showing a
summary of strand coverage. The left half of the segment of sequence
being displayed is covered
only by readings from one strand of the DNA, but the right half contains data
from both strands.
Along the top of the editor window is a row of command buttons
and menus. The rightmost pair of buttons provide help
and exit. To their left are two menus, one of which is currently in use. To
the left of this is a button which initially displays a search dialogue,
and then pressing it again, will perform the selected search.
Further left is the undo button:
each time the user clicks on this box the program reverses the previous edit
command. The next button, labelled "Cutoffs" is used to toggle between
showing or hiding the reading data that is of poor quality or is vector
sequence. In this figure it has been activated, revealing the poor quality
data in light grey. Within this, sequencing vector is displayed in
lilac. The next button to the left is the Edit Modes menu
which allows users to select which editing commands are enabled. The
next command toggles between insert and replace and so governs the effect of
typing in the edit window. The 2 entryboxes on the left hand side labelled
C and Q set the consensus and quality cutoff values
(see section Consensus and Quality Cutoffs).
One of the readings contains a yellow tag, and elsewhere some bases are
coloured red, which indicates they are of poor quality. The Information Line
at the bottom of the window can show
information about readings, annotations and
base calls. In this case it is showing information about the reliability of
the base beneath the editing cursor.
A better way of displaying the accuracy of bases is to shade their
surroundings so that the lighter the background the better the data.
In the figure above, this grey scale encoding of the base accuracy or
confidence has been activated for bases in the readings and the
consensus. This
screenshot also shows the Contig Editor displaying disagreements and edits.
Disagreements between the consensus and individual base calls are shown
in dark green. Notice that these disagreements are in poor
quality base calls. Edits (here they are all pads) are shown with a
light green background. When they are present, replacements/insertions
are shown in pink, deletions in red and confidence value changes in purple.
The consensus confidence takes into account several factors, including
individual base confidences, sequencing chemistry, and strand coverage.
It can be seen that the consensus for
the section covered by data from only one strand has been calculated to
be of lower confidence than the rest. The Status Line includes two
positions marked with exclamation marks (!) which means that the
sequence is covered by data from both strands, but that the consensus
for each of the two strands is different.
The Information Line at the bottom of the window is showing
information about the reading under the cursor: its name, number,
clipped length, full length, sequencing vector and BAC clone name.
The Contig Editor can rapidly display the traces for any reading or set
of readings. The number of rows and columns of traces
displayed can be set by the user. The traces scroll in register with one
another, and with the cursor in the Contig Editor. Conversely, the
Contig Editor cursor can be scrolled by the trace cursor.
A typical view is shown below.
This figure is an example of the Trace Display showing three traces
from readings in the previous two Contig Editor screendumps.
These are the best two traces from each strand plus a trace from a
reading which contains a disagreement with the consensus. The program
can be configured to automatically
bring up this combination of traces for each
problem located by the "Next search" option.
The histogram or vertical bars plotted top down show the confidence
value for each base call. The reading number, together with the direction of
the reading (+ or -) and the chemistry by which it was determined, is given at
the top left of each sub window. There are three buttons ('Info', 'Diff', and
'Quit') arranged vertically with X and Y scale bars to their right. The Info
button produces a window like the one shown in the bottom right hand
corner. The Diff button is mostly used for mutation detection, and causes a
pair of traces to be subtracted from one another and the result plotted, hence
revealing their differences. (see section Traces).
![[picture]](contig_editor.screen.unix.gif.html)
(Click for full size image)
![[picture]](contig_editor_grey_scale.unix.gif.html)
(Click for full size image)
![[picture]](contig_editor.traces.unix.gif.html)
(Click for full size image)
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Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_47.html