AMX DESIGN XPRESS V 1.5 - PROGRAMMER GUIDE Instrukcja Użytkownika Pobierz pdf (Strona 19)

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

Chapter 2 Designing Primers and Probes for Quantification Assays

Automatically Designing Primers and Probes

12 Primer Express Software 3.0 Getting Started Guide

Notes

Evaluating the candidate primer and probe sets:

The Location section of the Primers/Probes tab illustrates the location of the primers and

probes within the sequence. The number above the line is the starting base; the number

below the line is the ending base. Note that you can also see the corresponding location

of a selected candidate Primer/Probe set in the Sequence tab.

In the Sequence tab, the probe will be highlighted in pink, the forward primer in blue,

and the reverse primer in yellow. These default color designations can be changed by

clicking Tools > Options. If you place your cursor over any of these annotations, a tool

tip will appear showing the name of the annotation (Probe, Forward Primer, Reverse

Primers) start and end locations, Tm and %GC.

As a general guideline, select the primer/probe sets with a low Penalty score and a low

amplicon length (if the Penalty score and Amplicon Length fields are not displayed,

scroll to the right in the table). However, all primer/probe sets generated using default

parameters meet primer and probe guidelines. For more information regarding Penalty

scores, see Primer Express Software Version 3.0 Online Help.

Note: After the software finds primers and probes, the sequence box is locked. To edit

the sequence, click to unlock.

Saving the

Document

Select File > Save As to save the document for future use.

Ordering Primers

and Probes

To order your selected primers and probes, refer to Chapter 4, “Ordering Primers and

Probes.”

IMPORTANT! Before running your samples, Applied Biosystems recommends that you

run control samples to verify the performance of the selected primers and probes.

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