first previous next last contents

Template Display

The Template Display can show schematic plots of readings, templates, tags, restriction enzyme sites and the consensus quality. It can be used to reorder contigs, create tags and invoke the Contig Editor. It is invoked from the main gap4 View menu.

An example showing all these information types can be seen in the Figure below.

(Click for full size image)

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 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 indicate the relative orientation and separation of the contigs).

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. Zooming is available. 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.


As seen in the dialogue above, users can choose to display a single contig, all contigs, or a subset of contigs from a file of filenames ("file") or a list ("list"). If either the file or list options are chosen, the "browse" button will be activated and can be used to call up a file or list browser dialogue.

The items to be shown in the initial template display can be selected from the list of checkboxes. The default is to display all templates and readings. However, it is possible to display only templates with more than one reading ("Ignore 'single' templates) or templates with both forward and reverse readings ("Show only read pairs"). These latter two options may be beneficial if the database is very large.

In the section below we give details about the individual components of the overall Template Display.

first previous next last contents
This page is maintained by staden-package. Last generated on 22 October 2002.