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PrimerPlex, Oligo Design for Multiplex PCR & High Throughput SNP Genotyping and Analysis
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Comprehensive Assay Support

Using PrimerPlex, design oligos for multiplex PCR, ASPE and direct hybridization assays. The oligos are screened for cross reactivity to ensure high signal strength, minimizing Tm mismatches. The program not only designs oligos for detecting for the sequences, but enables you to design their corresponding amplifying primer pairs as well. The oligos are screened for dimers, runs and repeats.

Multiplex PCR Primer Design

Designing primer sets that work well for a multiplex assay can be a challenging task. PrimerPlex uses innovative and proprietary algorithms to design optimal multiplex primer sets, minimizing Tm mismatches. All sets are analyzed for cross reactivity to ensure specific and efficient amplification. You can choose the set best suited for your experimental needs from a list of alternates presented in variously sortable order. Using PrimerPlex, you have the flexibility of designing primers either towards the 3' end, the 5' end, at a specified distance from these ends or anywhere within the sequence.

For SNP genotyping assays, the program designs primers flanking mutations such as SNPs, DIPs (Deletion/Insertion Polymorphisms) and MNPs (Multiple Nucleotide Polymorphisms).

SNP Detection and High Throughput Genotyping

With PrimerPlex, you can design ASPE primers with the SNPs at the 3' end and capture probes with SNPs at their center. PrimerPlex enables you to detect all the mutations of a medium sized genomic sequence by designing oligos for each one of them. These primers and probes are checked for multiplexing and the best possible set is displayed.

Probe Specificity

The program BLAST searches multiple sequences in a single search run. The results are automatically interpreted and the homologies identified are avoided during probe design, ensuring that the design is highly specific.

Evaluate Primers and Probes

PrimerPlex can now use pre-designed well proven oligos to build a multiplex set. After specifying the oligos for each sequence, their properties are analyzed and the user is alerted for any deviations so found. For the sequences where pre-designed oligos are not available, PrimerPlex designs them, checks them for multiplexing and highlights compatibility issues if any. The user can then decide to accept the design or create a separate pool. This functionality gives complete control in the hands of the user.

Addition of xTAGs

The program now also supports a database of MagPlex TAGs along with the MicroPlex xTAGs (formerly known as FlexMAP TAGs) for automatic addition of appropriate tags to each sequence The tags are so chosen that they minimize dimerization and do not fold back on the oligos they are attached. In addition, a user can override the program's recommendation and select a tag on their own. PrimerPlex alerts the user if the tags are not unique or if the tag chosen is incompatible with the oligo. Tagging is available for Allele Specific Primer Extension (ASPE) primers.

Sequence View

The selected sequence can be viewed 3 or 10 bases per block, single stranded or double stranded. The designed primers and probes are marked, the sense primer in blue and the antisense primer in red. The selected SNPs are marked in green. Insertions are displayed as arrows pointing at the mutation position. For substitutions, the wild bases are highlighted.

Data Export

The data is exported in tab delimited format or as an html page for easy ordering or loading to a central database. It also exports the BLAST results in XML format.


Allows creation of multiple projects. A large amount of data can be easily organized and managed by creating a separate project for each experiment.

Built-in Database

Maintains a local database for sequence information and search results.

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