Xpression Primer

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With this application you can locate the outer primers anywhere in the UTRs or in regions of no significant homology.




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Xpression Primer is a revolutionary tagged primer design tool for designing xpression cloning experiments. Use the sophisticated algorithm of Xpression Primer to design thousands of tagged primers for expression cloning systems such as Gateway, BD In-Fusion, epitope and TOPO Tools.

You can choose to amplify an entire ORF or generate N terminal or C terminal fusion proteins. Xpression Primer ensures that the reading frame of the amplified ORF is conserved. To work with other expression systems, simply add functional tags of your choice and design tagged primers.

To ensure the success of your PCR experiment, let Xpression Primer design nested tagged primers to amplify ORFs. You can locate the outer primers anywhere in the UTRs or in regions of no significant homology. Xpression Primer will BLAST your sequences, automatically interpret the results and design highly specific primers.

The tagged inner primer pair amplifies the PCR product generated by the outer pair with little or no non-coding regions. You can also choose from a list of alternate primers to better meet specific experimental needs.

The versatile algorithm of Xpression Primer can design optimal sequencing primers for multiple sequences in a single run. It picks forward primers across the amplicon at a specified interval and reverse primers staggered on the opposite strand. You can export the results for several popular well plate configurations.

Here are some key features of "Xpression Primer":

Tagged Primer Design
■ Design Primers: Design thousands of primer pairs optimized for Gateway, BD In-Fusion, TOPO and epitope systems or add functionally useful tags to design primers for any expression system.
■ Design nested primers: Design primers to successfully amplify ORFs with nested PCR. The outer primer is designed in the UTR in a region of no significant homology. The inner primer pair amplifies the PCR product generated by the outer primer pair.
■ Design primers for fusion products: Designs primer for generating N and C terminal fusion products with functionally useful tags.
■ Lightning Speed: Processes three hundred 10kb sequences in approximately 2 minutes.
■ Maintain reading frame: Automatically maintain the reading frame of the ORF to be amplified when adding tags.
■ Avoid termination codon: Automatically checks for inframe termination codon.

High Throughput Primer Search
■ Algorithm: Calculates primer Tm using nearest neighbor thermodynamic algorithm.
■ Primer Rating: Uses statistical optimization techniques to output only the best rated primer pair.
■ Comprehensive search criteria: Primers are screened for their thermodynamic properties as well as secondary structures.
■ Uniform conditions: Optimizes all primers in a single search run for uniform PCR cycling conditions.

Sequencing Primer Design
■ Design primers: Sequencing primers are designed across amplicons with a user defined interval between forward primers. Reverse primers stagger on the opposing strands.

Data and Database Management
■ Projects: Multiple projects can be created. Data of multiple experiments can be easily managed by creating separate project for each experiment.
■ Application Database: Maintains a local database for sequence information and search results.

Web Integration ■ Web Integration: Quickly retrieves batches of ORF sequences directly into the program from Entrez using accession numbers or GI numbers.

■ Input formats: Supports sequences in GenBank, and FASTA formats. GenBank and FASTA formatted files can contain multiple sequences for batch loading.
■ View output: Primer search results can be viewed and manipulated in any spreadsheet program like Microsoft Excel and Lotus123.
■ Load output: Tab delimited format of the output file can be easily loaded into any database.


■ CPU Pentium III
■ RAM 256 MB of available RAM
■ Hard Disk Drive Space 500 MB of available hard disk
■ Screen Resolution 800 X 600


■ Fully demonstrates every function and feature of the product, but limited to the sample data provided.
Last updated on July 6th, 2014
Xpression Primer - The main window of Xpression Primer allows users to view detailed sequence information along with the accession number.Xpression Primer - The View menu of Xpression Primer allows users to view all structures or to view more sequence details.Xpression Primer - The Analyze menu of Xpression Primer allows users to perform a tagged primer search or a BLAST search.Xpression Primer - The Tools menu of Xpression Primer allows users to access the reaction conditions window of the application.Xpression Primer - The Reaction Conditions window of Xpression Primer allows users to customize the concetration of different solutions.Xpression Primer - The Tagged Primer Search window of Xpression Primer allows users to customize different primer design options.

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