The current version of the gap4 editor contains very many options that are not needed for mutation data. Given sufficient demand a version tailored for mutation studies could be produced. For now it might make it easier to understand the program if its origin as a genome assembly program is borne in mind. Here we outline the options and settings relevant to mutation studies. The assignment of reference sequence and traces is described above. From the editor they can be set by right clicking on the reading names.
Gap4 enables segments of sequences to be annotated (or tagged). Each tag has a type (eg primer) and each type has an associated colour. Each instance of a tag can include editable text. This text can be viewed and edited by right clicking on the tag and selecting "Edit tag", after which a text box will appear. Gap4 can display annotations/tags as background colour and the user can specify which tag types are shown. For mutation studies the following tag types may usefully be activated, and all others turned off. Using the "Set Active Tags" option in the "Settings" menu first click on "Clear all". Then click on "primer". To add further types you must hold down the "Ctrl" key on the keyboard while clicking. Now scroll down and click on "Mutation", "Heterozygous" and "FEATURE CDS". Add any others required, then click "OK".
The following configurations are performed via the "Settings" menu.
Gap4 has three consensus generation algorithms. When using a reference sequence it is convenient if the consensus shown in the editor is forced to be the same as the reference. This will be the case if either the "Weighted base frequencies" or the "Confidence values" consensus algorithms are being used. This selection is made using the "Consensus algorithm" option.
Translations are shown in what gap4 refers to as the "Status" line. To enable automatic translation of the exons defined in the reference sequence, in the "Status Line" option set "Translate using feature tables".
To enable automatic display of trace diferences, in the "Trace Display" option set "Auto-Diff Traces".
To show only the base differences between the consensus/reference, set "Highlight Disagreements". These can be shown by dots or colour.
To show base confidence values set "Show reading quality" and also make sure that the value in the box labelled "Q" at the top left of the editor is set to 0 or greater.
To force forward and reverse reading pairs to be shown in adjacent records in the editor set "Group readings by templates" (NB this assumes that an appropriate naming scheme has been used).
If a reference sequence is assigned, the numbering at the top of the sequence will reflect the base positions in that sequence. Any pads in the reference sequence are ignored. If no reference sequence is assigned, the numbering will ignore pads if the "Show unpadded positions" option is activated.
At the bottom of the "Settings" menu is an option to "Save settings". Use of this will mean that the current configuration will be set automatically next time the editor is used (and hence the steps just described only need to be performed once).