I am trying to install Primer Express® Software, version 2.0 on my new computer with Windows® XP as the operating system. It is giving me an error message, "Could not open Primers Express Preferences, because there is not enough memory" when trying to install or open the software despite this being a new computer. What can I do?

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Answer

The Primer Express® 2.0 software was developed to work on Windows 2000 operating systems. The "not enough memory" error message is generated due to incompatibility with the newer processor in the computers and the algorithm of the Primer Express® v2.0 software. We have developed a patch to help over come this error message. You can download this patch from our website by going to the software downloads option under the Technical Resources page on our website. Click on ABI PRISM® 7000 Sequence Detection System, then click on the PC link next to Primer Express® P4 Enabler. Also download the installation instructions by clicking on the Read Me link.

Answer Id: E2479

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0b93f160acc0986f82ed773210bc601b_FAQ

When manually selecting primer and probe sequences using the Primer Express® software, is there a feature that can evaluate their compliance with Real-Time PCR primer and probe design guidelines?

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Answer

Yes, there is a feature to evaulate complaince of your primer and probe sequences. By copying and pasting the potential primer or TaqMan® TAMRA probe sequence into the Primer Test Document, you can get % G + C and melting temperature (Tm) information. The Primer/Probe Test can be found by going to TOOLS > PRIMER PROBE TEST TOOL.

If evaluating an MGB probe, you must use the TaqMan® MGB Quantification option. Guidelines for primer and probe design must be followed as outlined in the Primer Express® software v3.0 User Manual, which can be found in the Primer Express® software folder on your computer. You can find a copy on our website as well.

Answer Id: E2155

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5af94f2215d355331050fcae636b9cba_FAQ

I get the following message when trying to start the Primer Express® software: “Error opening Archive file: Primer Express is unable to open the archive file. Please move this file to another directory and run the Primer Express® software again to create a new Archive.” How do I solve this problem?

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Answer

This error message can occur while attempting to install the Primer Express software, or sometimes when launching the software after it has been installed on the computer. To create a new archive file, hold down Alt key (to the left of the space bar) while opening the Primer Express® application. You should get the browser window shown below. Click on “New” to create a New Archive.

The name “PXArchive” will automatically populate in the file name field. You may keep that name or change it to something different. Once you've named the Archive file, click on save. You should now be able to continue with the installation or use of the Primer Express Software.

Answer Id: E2156

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7e1aae0d1d60a205e73b8d0a7ab27a02_FAQ

Is there a User Manual for Primer Express® software?

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Answer

No. However, there is a Primer Express® User Manual and an Applications Tutorial that gets loaded into the Primer Express® software folder when the software is installed onto your computer. In addition, there is the Getting Started Guide: Primer Express® Software Version 3.0 and tutorials available on the Primer Express product page.

Answer Id: E1000

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54de7377e18d99fab5d0b1c7fdb0b42a_FAQ

In the Primer Express® software there is a category called the Penalty Score. What is the definition of the Penalty Score, and should I take it into consideration when picking primers and probes?

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Answer

When creating primer/probe sets, the Primer Express® software will assign each set a Penalty Score. This score is based on the percentage of the preferred parameters, as defined on the Parameters page, that are met by each design. However, since the TaqMan®-specific Primer/Probe Document only chooses primer/probe sets that meet the Parameters criteria, the penalty score is irrelevant in that case. The score does not and will not determine the primer/probe performance. When following the default parameters set up in the software, any of the primer and probes selected by the software should perform well when utilizing the universal cycling conditions and the TaqMan® Universal PCR Master Mix.

Answer Id: E1754

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0e2c78c61daf4e4cca0abf6d502637de_FAQ

What is a primer-dimer? Can I predict possible primer-dimers for a given primer set in the Primer Express® software?

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Answer

Primer-dimers, usually undesirable, result when one primer binds to the other primer and possibly gets extended. The main disadvantages of this is that there will be background sequence or signal in your PCR or Real-Time PCR results, and the primers become unavailable for binding to the true desired target sequence. To view potential primer-dimers from a selected primer set, go to "Options", and "Show Primer Secondary Structure". The Primer Express® software has built in features to exclude extensive primer dimer formation.

Answer Id: E1764

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e7e2307da2d658bc2840c95e0ae121e9_FAQ

How can I convert my sequence from the positive strand to the negative strand in Primer Express® software?

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Answer

Highlight the entire sequence. On the menu bar, go to Edit --> Copy Complement and paste it into a new sequence window.

Answer Id: E1794

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5b32d3234e4479356e8004165dfaf62a_FAQ

How can I create an additional Archive file in the Primer Express® software?

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Answer

When you launch the software, hold down the "Option" key on a Macintosh computer, or hold down the "Alt" key on a computer running a Windows OS. The dialog box will lead you to create a new archive file.

Answer Id: E1795

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f3cb10bd6b2cd8208cb5a17b474fb386_FAQ

How do I save the primers and probes listed in the Primers Tab search results in Primer Express® software?

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Answer

Click the Save button at the bottom of the Primers page. Open the saved tab delimited text file from within a spreadsheet program, such as Microsoft® Excel® software. You may view and modify the file here.

Answer Id: E1796

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41dbe77b7b4df7dfcc1e6f72a41a0d4c_FAQ

Within the Primer Express® software, what is a "GC Clamp" and what is its impact if I have a GC Clamp at the end of a primer?

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Answer

"GC Clamp" is the number of G or C residues at the 3' end of a primer. In the Primer Express® software, the GC Clamp can be set to any value, including zero (which is the default). In some cases, a GC Clamp of greater than three will cause no primers to be chosen. When designing primers and probes for Real-Time PCR it is recommended not to have a GC clamp on the 3' end of the primers.

Answer Id: E1797

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d5e0bb2e7c0944a0999ea1c973c95d40_FAQ

Where can I find a selected amplicon melting temperature in Primer Express software?

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Answer

You can find the amplicon in the Amplicon Tm column in the Primers and Probes Tab window.

Answer Id: E1798

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dd724668a8bc2c5715ad5c3241021a14_FAQ