Alignment-based primer and probe design

CLC Genomics Workbench allows the user to design PCR primers and TaqMan probes based on an alignment of multiple sequences.

The primer designer for alignments can be accessed with:

        Toolbox | Molecular Biology Tools (Image lab_work_support) | Primers and Probes (Image primersandprobes)| Design Primers (Image primerdesign)

Or if the alignment is already open, click Primer Designer (Image alignment_primerdesign) in the lower left part of the view.

In the alignment primer view (see figure 18.12), the basic options for viewing the template alignment are the same as for the standard view of alignments (see View sequences for an explanation of these options). This means that annotations such as known SNPs or exons can be displayed on the template sequence to guide the choice of primer regions.

Image initialprimerview_alignments
Figure 18.12: The initial view of an alignment used for primer design.