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 (
) | Primers and Probes (
)| Design Primers (
)
Or if the alignment is already open, click Primer Designer (
) in 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). This means that annotations such as known SNPs or exons can be displayed on the template sequence to guide the choice of primer regions.
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