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Introduction

The template display provides a graphical overview of a set of contigs. This information includes readings, templates, tags, restriction enzyme sites and quality calculations. In the figure below all of these information types can be seen.

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(Click for full size image)

The large top section contains the readings shown as short arrowed lines, and the templates shown as longer (mostly blue) lines. Beneath this are rulers; one for each contig. These ruler lines may be staggered vertically. Beneath them is the quality plot. At the bottom is the restriction enzyme plot. The quality and restriction enzyme plots for each contig are displayed in separate windows. The coloured blocks immediately above and below the ruler are tags. These tags can also be seen on their corresponding readings in the large top section. The usual zooming mechanism 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.

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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.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_75.html