Overview of using a motif
Traditionally, alignment is focused on minimizing the number of mismatches between the reference and a sample read, or a “best fit” alignment; however, because forensic analysis has established conventions for the position of many common variants, this traditional approach to alignment is not always preferred when analyzing mtDNA. As a result, GeneMarkerHTS provides the option of using a motif to better meet your analysis requirements. A motif is a list of variant calls within a specified region that are translated into an expected sequence. You define this list of variant calls in a motif file, which is a text (.txt) file that has the following format:
• The first line for each motif definition in the file is preceded with a hash tag/pound symbol (#) and this line identifies the start and end points for the region.
• The variant calls in the motif file are listed with standard forensic nomenclature, for example, Deletion: 16191d, Insertion: 16193.1C, and SNP: 1184A.
When you are creating a motif file, note the following:
• Spacing of the variants is not absolute, but you must use commas to separate the variant calls.
• Regions cannot overlap.
• No two motifs in the same region can resolve to the same sequence.
If you elect to use motif alignment, then the alignments of reads that cross motif regions with expected sequences are adjusted to match the list of variants. Reads that start or end in motif regions are soft-clipped. You can use the default motif that is supplied with GeneMarkerHTS, or you can use an existing custom motif to create and/or edit your own custom motifs. See To create or edit a custom motif.
 | When creating a custom motif, you can use the default version that is supplied with Version 2.6 of GeneMarkerHTS as your starting point, or you can use a prior version. All prior versions of the default motif are found in the Resources folder in the installation directory for GeneMarkerHTS. |