AMX DESIGN XPRESS V 1.5 - PROGRAMMER GUIDE Manuale Utente Scaricare il pdf (Pagina 20)

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December 16, 2004 3:54 pm, GSG_Chapter_4-02.fm

Chapter 2 Designing Primers and Probes for Quantification Assays

Manually Designing Primers and Probes

Primer Express Software 3.0 Getting Started Guide 13

Notes

Manually Designing Primers and Probes

You may choose to manually design primers and probes for various reasons:

• Automated primer/probe design did not find primers and probes.

• To design a probe over an exon junction.

• To design a probe for DNA sequence homologs.

• To design primers and probes according to your own specifications.

Creating a

Quantification

Document

Create a Quantification document and load a sequence file as you would for automatic

primer/probe set design. See “Creating a Quantification Document” on page 9.

Manually

Designing the

Probe

1. Select a putative probe region containing at least 25 bases.

2. Copy (Ctrl+C) the sequence.

IMPORTANT! The Primer Probe Test Tool eliminates non-ATCG bases. Before copying

a sequence, change any non-ATCG bases, or select a different region of the sequence.

3. Select Too ls > P rime r Probe Te st Too l. The Primer Probe Test Tool dialog box

appears (see “Figure 4. Primer Probe Test Tool dialog box” on page 14).

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AMX DESIGN XPRESS V 1.5 - PROGRAMMER GUIDE Manuale Utente Pagina 20