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Using The Gap4 Editor With Mutation Data

The current version of the editor has a fixed width and a maximum height. If too many sequences are present at any position a vertical scrollbar on the right edge can be used to move them up and down. The CONSENSUS line will always be visible, but at present, the reference sequence is scrolled along with all the other sequences and so may disappear. Horizontal scrolling is achieved in the usual ways, plus by use of the >, >> and <, << buttons. The reading names can be moved left and right using the scrollbar above them.

Configure the editor as described above.

The traces for readings (and their reverse) can be examined over their full length one at a time by simply double clicking on them then scrolling along. Any mutations observed can be labelled by right clicking on the base in the editor display and invoking the "Create tag" option. This brings up a dialogue box. At the top is a button marked "Type:comment"; clicking on this will bring up another dialogue with a list of all the tag types; choose the appropriate one ("Heterozygous" or "Mutation"). There are obviously many advantages to examining the traces like this using gap4. However, if the automated mutation detection methods are trusted, or used in way that makes them trustworthy for the type of study being undertaken, then there are quicker ways of examining the data.

The "Next Search" button at the top of the editor gives access to many types of search, one of which is "tag type". If this is selected a button appears labelled "Tag type COMM(Comment)". Clicking on this will bring up a dialogue showing all the available tag types. If the user selects, say "Mutation", each time the "Next Search" button is used the program will position the editing cursor on the next mutation tag. Double clicking will automatically bring up the appropriate traces as shown in figures 1, 2 and 5 (see section Introduction to mutation detection). The user can view the traces and if necessary alter the tag (eg delete it if it is a false positive).

Once all the data has been checked and all mutations and heterozygous bases have been tagged a report can be generated using the "Report Mutations" option in the editor "Commands" menu. Note that it is also possible to simply report all differences between base calls and the reference, but the usual procedure is for the program to report all bases tagged as "Mutation" or "Heterozygous". Example output is shown above in Figure 6 (see section Introduction to mutation detection). The report appears in the gap4 "Output window" which can be saved to disk by right clicking on the text and selecting "Output to disk".

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This page is maintained by staden-package. Last generated on 22 October 2002.