PrimerPlex 2.00

PrimerPlex can be used on systems such as Luminex 100, Luminex 200 and Bio-Plex 200. Based on Luminex xMAP technology, these systems offer a versatile platform for multiplex nucleic acid detection in the 96-well format.
PrimerPlex designs specific capture probes for direct hybridization assays and primer pairs for Allele Specific PCR Extension (ASPE) assays. The assays are used for high throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping.
To ensure specificity, the oligos are designed after avoiding the regions of homologies identified by BLAST search.
PrimerPlex then checks the oligos for cross homologies and minimizes Tm mismatches to give you the best possible multiplex set.
In the process, it will quickly analyze millions of possible multiplex sets in an a few seconds. PrimerPlex will then present a list of alternate sets to you as well.

Main 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.

System requirements:
- Power PC G5 1.6 GHz or Intel 1.8 GHz Intel Core Duo
- 256 MB of available RAM
- Hard Disk Drive Space 500 MB
- Screen Resolution 800 X 600

Enhancements
- 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.
- The program now also supports a database of 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 programs 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 both, Allele Specific Primer Extension (ASPE) primers and capture probes.
- Amongst a host of other improvements, PrimerPlex can now design oligos for all the SNPs of a medium to large sized genomic sequences. If an oligo overlaps with another, or if it spans another SNP, an overlapping report is generated along with the design results which serves as a reference. The program now supports rsID sequences (in addition to ssIDs), mutations such as DIPs (Deletion/Insertion Polymorphisms), MNPs (Multiple Nucleotide Polymorphisms) and mixed mutations (a sequence with multiple variants for a given allele) etc.