PrimerPlex

What's new in this version

Features

Comprehensive Assay Support:
Using PrimerPlex, design oligos for ASPE and direct hybridization assays. Both the assays are multiplex assays. The probes for both the assays are screened for cross homologies to ensure high signal strength. 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.

SNP Detection and Genotyping:
With PrimerPlex, you can design ASPE primers with the SNP at the 3' end and capture probes for direct hybridization assays.

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.

Multiplex PCR Primer Design: Designing multiplex primer sets that work well can be a challenging task. PrimerPlex uses innovative and proprietary algorithms to design optimal primer sets, minimizing Tm mismatches, for up to 100 targets for working in a single tube multiplex assays. All sets are analyzed for cross compatibility and cross homology to other targets 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 the SNPs. Included is the ability to specify the distance of the primers to bind upstream or downstream of a SNP.

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.

Projects:
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.