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

Upgrades

PrimerPlex 2.72 Released

The latest changes to the genomic databases at the NCBI-BLAST along with fixes to reported problems are accommodated.

PrimerPlex 2.71 Released

The upgrades accommodates latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems.

The version is now compatible with Mavericks, Mac OS X 10.9.

PrimerPlex 2.70 Released

The upgrade accommodates the latest genomic databases available at the NCBI BLAST server and fixes to reported problems. The version is now compatible with Windows 8.

PrimerPlex 2.62 Released

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

The upgrade offers compatibility with Windows 64bit OS.

PrimerPlex 2.61 Released

The upgrade offers compatibility with Lion, Mac OS X 10.7.

The latest changes at the NCBI BLAST, including latest genomic databases and fixes to reported problems are also accommodated.

PrimerPlex 2.60 Released

PrimerPlex now supports the MagPlex TAGs in addition to the Microplex xTAGs. Use of MagPlex TAGs eliminates the separate step of coupling content specific probes to the MagPlex microspheres. The TAG addition is instrument specific. A user can choose an instrument based on the number of sequences being multiplexed. PrimerPlex will make instrument specific TAGs available for tagging.

The TAGs are automatically appended with the ASPE primers, checked for their uniqueness and their secondary structure formations, to avoid minimal cross reactivity with the oligo and assuring success in a multiplex reaction. Users can override the program's recommendations and append the TAGs as per their requirements as well.

PrimerPlex 2.50 Released

The new version now supports designing of multiplex primers for standard PCR assays. The algorithms runs through hundreds of primer sets to find primers that not only work efficiently for the sequence but also do not cross hybridize with any other sequence in the pool, or interact with other primer sets of other sequences to assure high signal strength.

The design parameters have now been optimized, based on empirical and theoretical evidence, to improve the success in a multiplex reaction. Primers for standard multiplex PCR are designed for different amplicon lengths, different enough to form discernible bands when visualized on a gel.

The facility to locate primers in the region of your interest by specifying a search range in the templates chosen for multiplexing has also been included.

The latest genomic databases available at the NCBI BLAST server are also supported.

PrimerPlex 2.11 Released

Includes fixes to the reported problems.

PrimerPlex 2.10 Released

PrimerPlex now offers compatibility with Snow Leopard, Mac OS X 10.6.2. The upgrade also accommodates the latest changes at the NCBI BLAST server including support for the latest genomic database.

PrimerPlex 2.00 Released

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 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.

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.

PrimerPlex 1.01 Released

PrimerPlex now offers compatibility with Leopard, Mac OS X 10.5. The upgrade also accommodates the latest changes at the NCBI BLAST server including support for the latest genomic database.

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