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:
select alignment | Toolbox | Primers and Probes (
)| Design Primers (
) | OK
or If the alignment is already open: | Click
Primer Designer (
) at the lower left part
of the view
In the alignment primer view (see figure 17.12), 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 SNP's 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.
Figure 17.12: The initial view of an alignment used for primer design.
Subsections
- Specific options for alignment-based primer and probe design
- Alignment based design of PCR primers
- Alignment-based TaqMan probe design