Alignment-based primer and probe design

CLC Main 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 in two ways:

        Toolbox | 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 19.12), 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.

Note! This means that annotations such as e.g. known SNPs or exons, can be displayed on the template sequence to guide the choice of primer regions. Since the definition of groups of sequences is essential to the primer design, the selection boxes of the standard view are shown as default in the alignment primer view.

Image initialprimerview_alignments
Figure 19.12: The initial view of an alignment used for primer design.