The Template Display can show schematic plots of readings, templates, tags, restriction enzyme sites and the consensus quality. Colour coding distinguishes reading, primer and template types. The Template Display can also be used to reorder contigs and to invoke the Contig Editor.
An example showing all these information types can be seen in the Figure below.
The large top section contains lines and arrows representing readings
and templates. Beneath this are rulers;
one for each contig, and below those is the quality plot.
The template and reading section of the display is in two parts. The top
part contains the templates which have been sequenced from both ends but
which are in some way inconsistent - for example given the current
relative positions of their readings, they may have a length that is
larger or greater than that expected, or the two readings may, as it
were, face away from one another. Colour coding is used to distinguish
between different types of inconsistency, and whether or not the
inconsistency involves readings within or between contigs. For example,
most of the problems shown in the screendump above are coloured
dark yellow, indicating an inconsistency between a pair of contigs.
The rest of the data, (mostly dark blue indicating templates sequenced
from only one end), is plotted below the data for the inconsistent
templates.
Forward readings are light blue and reverse readings are orange.
Templates in bright yellow have been sequenced from both ends, are consistent and
span a pair of contigs (and so indicating the relative orientation and
separation of the contigs).
At the bottom is the restriction enzyme plot.
The coloured blocks immediately above and below the ruler are tags.
Those above the ruler
can also be seen on their corresponding readings in the large top
section.
The display can be zoomed. The position of a crosshair
is shown in the two left most boxes in the top right hand corner.
The leftmost
shows the distance in bases between the crosshair and the start of the
contig
underneath the crosshair. The middle box shows the distance between the
crosshair and the start of the first contig. The right box shows the
distance
between two selected cut sites in the restriction enzyme plots
(see section Template Display).
![[picture]](template.display.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_8.html