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Applied Biosystems™ Primer Express™ Software v3.0.1 License

Catalog No. 4363993
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Description

Primer Express™ Software v3.0.1 License

The Primer Express™ Software v3.0.1 allows you to design your own primers and probes using TaqMan™ and SYBR™ Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed specifically for use with our StepOne™, StepOnePlus™, 7300, 7500, 7500 Fast, 7900HT, ViiA™ 7, and QuantStudio™ real-time PCR systems, Primer Express™ Software provides customized application-specific documents for absolute⁄relative quantitation and allelic discrimination.

  • Enables individual oligonucleotide design for real-time PCR applications.
  • Supports assays based on TaqMan™ and SYBR™ Green I dye chemistries.
  • Provides design flexibility, ease-of-use, and requires minimal optimization.
  • Provides robust assay performance when used in accordance with Rapid Assay Development Guidelines (RADG).

    Easy-to-Learn Software
    The Primer Express™ Software v3.0.1 is flexible, easy to learn and to use, and requires minimal optimization. It includes an algorithm optimized specifically for use with TaqMan™-based reagents, recommended primer⁄probe concentrations, and default thermal cycling conditions. Primer Express™ Software also supports assays based on the SYBR™ Green I dye. This minimizes the need for assay optimization and streamlines the design process.

    The software also allows customized designs if the probe and⁄or one or more primers are known. Default and adjustable parameters (Figure 1) provide the flexibility required for all users, regard

    Simple to Use
    Simplicity and flexibility are the hallmarks of Primer Express™ Software v3.0.1, which is fully compatible with all StepOne™, StepOnePlus™, 7300, 7500, 7500 Fast, 7900HT, ViiA™ 7, and QuantStudio™ real-time PCR systems. Whether your research includes gene quantitation or allelic discrimination studies, Primer Express™ Software belongs in your lab.

    Automated and Manual Primer⁄Probe Design
    The Primer Express™ Software v3.0.1 will design your primers and probes automatically, or you can design them manually. For automated design, simply choose either TaqMan ™ or TaqMan™ MGB assays. If you know the sequence, you need only to import (or copy and paste) the sequence and quickly view your results. Alternatively, if you prefer to design the primers and probes manually, the procedure is equally simple and straight-forward as well.

    Rapid Assay Development Guidelines
    The Primer Express ™ Software v3.0.1 was designed with our Rapid Assay Development Guidelines (RADG). The RADG are a simple yet comprehensive set of guidelines for use with our real-time PCR instruments and reagents. Many traditional variables, including magnesium chloride concentration and the thermal cycling protocol itself, have been standardized, which substantially reduces assay development time.

    For Research Use Only. Not for use in diagnostics procedures.

    • Specifications

    Content And Storage Store at Room Temperature, Included w/ StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, QuantStudio 6, QuantStudio 7, and QuantStudio 12k Flex, Runs computers on Windows 10 OS for 7500, 7500 Fast, QuantStudio 6, QuantStudio 7, and QuantStudio 12K Flex instruments, Runs computers on Windows XP OS for StepOne, StepOnePlus, 7300, 7900HT, and ViiA 7 instruments, Runs on Windows 7 32-bit or Windows XP OS for non-instrument-controlling computers
    For Use With (Equipment) 7300 System, 7500 Fast System, 7500 System, QuantStudio™ 12k Flex, QuantStudio™ 6 Flex, QuantStudio™ 7, StepOne™, StepOnePlus™, ViiA™ 7 System
    Product Line Primer Express
    Software Type Primer Design
    Product Type License
    For Use With (Application) Real Time PCR (qPCR)
    Operating System Windows 10
    Quantity 5 users

    Frequently Asked Questions (FAQs)

    I need to see all the primer and probe sequences from an assay design right away. How can I do this?

    You can directly see all the primer and probe sequences from a test design right away using the Primer Express Software. Open the software and choose File => New. Choose either TaqMan MGB Quantification or TaqMan Quantification for Gene Expression Assay design. Copy/paste your gene sequence of interest into the new window and click on the green triangle to get primer/probe designs.
    Can I use Primer Express software on Windows 10?

    Yes, you can use Primer Express v3.0.1 on Win10 computers.
    When designing primer and probes, what is difference between green amplicons and red amplicons in the "Map" display of Primer Express 2.0 software?

    Primer and probe sets that satisfy the optimal length and Tm requirements are in red. Sets that don't satisfy one or the other or both of these parameters are in blue or green.
    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?

    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.
    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?

    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.
    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?

    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.

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

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

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

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

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

    Highlight the entire sequence. On the menu bar, go to Edit --> Copy Complement and paste it into a new sequence window.
    What does "Ta" mean in the Amplicon column-Primers Tab window of the Primer Express Software?

    Ta is the annealing temperature of a DNA fragment (amplicon or primer).
    What is a primer-dimer? Can I predict possible primer-dimers for a given primer set in the Primer Express software?

    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.
    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?

    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.

    Can I use Primer Express on my Windows 11 computer?

    Primer Express is an older program and as such we have not validated it for use on Windows 11 systems. Primer Express v3.0.1 is validated on Windows 10. Limited testing has shown that it does appear to run on Windows 11 computers, however we cannot guarantee this for all systems. For the computers that we have tried it on, the installation proceeded without any errors, but to run the program, it was necessary to use the “Compatibility” function in Windows and choose “Win10”. Please be aware that we would not be able to assist with troubleshooting the installation beyond the comments above.
    When manually selecting primer and probe sequences in the Primer Express software, is there a feature that can evaluate their compliance with TaqMan chemistry requirements?

    By cutting and pasting the desired sequence into the Primer Test Document in Primer Express software, you can get %G + C and melting temperature (Tm) information. This is found by going to FILE > NEW > PRIMER TEST DOCUMENT. You must still make sure to follow all the guidelines for primer and probe design that are outlined in the Help menu.
    Is there a User Manual for Primer Express software?

    Yes, 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 (http://tools.thermofisher.com/content/sfs/manuals/cms_041902.pdf) and tutorials available on the Primer Express product page.

    For Research Use Only. Not for use in diagnostic procedures.