To create or edit a custom motif
 | Although you can manually edit a motif file, SoftGenetics strongly recommends that you use the built-in Motif Editor instead. |
1. On the New Project dialog box, do one of the following:
Option | Description |
|---|---|
Create Motif: Use the default motif that is supplied with GeneMarkerHTS as your starting point for creating a custom motif. | 1. Ensure the Use Default Motif is cleared and that under Alignment Options, Motifs is selected. 2. Click Create Motif. The Motif Editor dialog box opens. The built-in (default) motif is loaded in the dialog box. Expected variant calls are highlighted in gray. Tip: Beginning with V2.0.6 of GeneMarkerHTS, the default motif that is supplied with GeneMarkerHTS has been updated. You can, however, use a prior version of the default motif. All prior versions of the default motif are found in the Resources folder in the installation directory for GeneMarkerHTS. |
Edit Motif: Create a custom motif by editing an existing custom motif. | 1. Ensure the Use Default Motif is cleared and that under Alignment Options, Motifs is selected. 2. Next to the Motif Path field, click the Browse button to open the Open Motif dialog box, and then browse to and select the custom motif. 3. Click Edit Motif. The Motif Editor dialog box opens. The selected custom motif is loaded in the dialog box. Expected variant calls are highlighted in gray. |
2. For each motif region, do any or all of the following:
Option | Description |
|---|---|
Update range | Adjust the Start and/or End values for a motif region (manually edit the values, or use the Up Arrow/Down Arrow buttons to adjust the value one base at a time), and then click Update Range. Tip: Because motifs require exact matches, shorter motifs are better for alignment. |
Add Motif | Adds a new motif as the last in the list of displayed motifs for the region. The default sequence for a new motif is always set to the reference sequence. |
Remove Motif | Select a motif, and then click to remove the selected motif from the motif region. |
Remove Region | Click to remove a region entirely from the motif. |
3. If you are done with customizing the motif, then continue to Step 4; otherwise, optionally, to add one or more regions to the motif, do the following:
a. Click Add Region.
A blank new region placeholder is displayed at the bottom of the Motif Editor dialog box.
 | Use the scroll bar on the right side of the dialog box to scroll to the bottom of the dialog box and view the placeholder region. |
b. Specify the start and end positions for the new region, and then click Update Range.
c. Create the needed motifs for the new range. (See Step 2.)
4. Optionally, to check for errors before saving the customized motif, click Check For Errors; otherwise go to Step 5.
If errors exist in the customized motif, then a Motif File Errors dialog box that details the errors in the motif file opens; otherwise, the Motif File Errors dialog box displays the message “No Errors.”
5. Click OK to close the Motif File Errors dialog box.
• If the file did not contain any errors, then continue to Step 6.
• If the file did contain errors, then iteratively correct the file and click Check For Errors until you receive the message “No Errors,” and then continue to Step 6.
6. To save the new motif file, click Save As.
The Save Motif dialog box opens. The file format is set to .txt and you cannot edit this.
7. Specify the name for the motif file, and then browse to and select the location in which to save the file, and then click Save.
The Save Motif dialog box closes. The Motif Editor dialog box remains open.
8. Click “X” to close the Motif Editor dialog box.
You return to the New Project dialog box. The full path to the customized motif file, including the file name, is displayed in the Motif Path field. You can now use the motif for mtDNA analysis.