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Introduction

Gap commands such as Find Internal Joins (see section Find Internal Joins), Find Repeats (see section Find Repeats), Check Assembly (see section Check Assembly), and Find Read Pairs (see section Find Read Pairs) automatically transform the Contig Selector (see section Contig Selector) to produce the Contig Comparator. To produce this transformation a copy of the Contig Selector is added at right angles to the original window to create a two dimensional rectangular surface on which to display the results of comparing or checking contigs. Each of the functions plots its results as diagonal lines of different colours. If the plotted points are close to the main diagonal they represent results from pairs of contigs that are in the correct relative order. Lines parallel to the main diagonal represent contigs that are in the correct relative orientation to one another. Those perpendicular to the main diagonal show results for which one contig would need to be reversed before the pair could be joined. The manual contig dragging procedure can be used to change the relative positions of contigs. See section Changing the Contig Order. As the contigs are dragged the plotted results will be automatically moved to their corresponding new positions. This means that if users drag the contigs to move their plotted results close to the main diagonal they will be simultaneously putting their contigs into the correct relative positions.

Because this plot can simultaneously show the results of independent types of search, users can see if different analyses produce corroborating evidence for the ordering of contigs. Also if a result from Check Assembly lies on the same horizontal or vertical projection as a result from Find Repeats, users can see the alternative position to place the doubtful reading. Ie this is an indication that a reading may have been assembled in an incorrect position.

By use of popup menus the plotted results can be used to invoke a subset of commands. For example if the user clicks the right mouse button over a result from Find Internal Joins a menu containing Invoke Join Editor (see section The Join Editor) and Invoke Contig Editors (see section Editing in gap4) will pop up. If the user selects Invoke Join Editor the Join Editor will be started with the two contigs aligned at the match position contained in the result. If required one of the contigs will be complemented to allow their alignment.

A typical display from the Contig Comparator is shown below. It includes results for Find Internal Joins in black, Find Repeats in red, Check Assembly in green, and Find Read Pairs in blue. Notice that there are several Find Internal Joins, Find Read Pairs and Find Repeats results close to the main diagonal near the top left of the display, indicating that the contigs represented in that area are likely to be in the correct relative positions to one another. In the middle of the bottom right quadrant there is a blue diagonal line perpendicular to the main diagonal which indicates a pair of contigs that are in the wrong relative orientation. The crosshairs show the positions for a pair of contigs. The vertical line continues into the Contig Selector part of the display, and the position represented by the horizontal line is also duplicated there.

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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_40.html