Oligo Design for High Throughput SNP Genotyping, SNP Analysis & More...

PrimerPlex is an efficient and sophisticated tool for designing multiplex oligos for multiplex analysis platforms such as Luminex 100, Luminex 200, Bio-Plex 200 suspension array systems. Based on Luminex Corporation’s xMAP® technology, these systems offer a versatile platform for multiplex nucleic acid detection in a 96-well format.

PrimerPlex designs specific capture probes for direct hybridization assays and primers for Allele Specific PCR Extension (ASPE), for multiplexed high throughput SNP genotyping applications such as SNP analysis, pathogen detection, strain typing, and haplotyping. The oligos are designed after avoiding the regions of homology identified by a BLAST search.

PrimerPlex checks the oligos for cross homologies and minimizes Tm mismatches to give you the best possible multiplex set. In the process, it analyzes millions of possible multiplex sets in a flash. In addition, PrimerPlex presents a list of alternate sets for you to choose from, based on your specific experimental needs.

Design Options

Direct Hybridization Assays:
PrimerPlex designs optimal allele specific capture probes for direct hybridization assays. The probes are designed such that the SNPs are at their centers. Our innovative and proprietary algorithm analyzes each of these probes for their suitability in a multiplex reaction. The probes are screened for cross and self dimers, assuring strong signal strength.
This functionality makes PrimerPlex the only software product capable of designing probes for 100 individual targets in a single tube multiplex reaction. Also included is the ability to design compatible primer pairs for amplifying the template.
A series of probes can also be designed for detecting variable sites of a particular gene. For such cases, PrimerPlex designs equal length capture probes after BLAST searching the sequences and avoiding the regions of homology.

ASPE Assays:
Another approach to detect SNPs is to use a solution-based sequence specific enzymatic reaction such as ASPE to determine the target genotype.
PrimerPlex designs highly specific primers for multiplexed ASPE assays. The ASPE primers are designed such that the SNP lies at their 3' end.
PrimerPlex also designs primers to amplify the target sequence for ASPE assays. The primers could be designed for a multiplexed reaction as well.

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.