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MSRE-HTPrimer

Designs all possible PCR primer pairs and oligos, followed by filtering for single nucleotide polymorphisms (SNPs) loci and repeat regions. MSRE-HTPrimer is an open-source, portable, web-based use pipeline, which facilitates the design of primer pairs for epigenetic and genomic target validation studies. It uses a simple input and output model and can design primers for hundreds to thousands of target sequences in a single run. It annotates all resulting primer pairs extensively by adding genetic and epigenetic information including SNPs, RefSeq genes, repeats, and CpG islands.

EvOligo

Offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user. EvOligo is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. It applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions.

MultiPLX

Provides a tool for automatic grouping of polymerase chain reaction (PCR) primers for multiplexed PCR. MultiPLX performs grouping by calculating many important interaction levels between the different primer pairs and then distributes primer pairs to groups so that the strength of unwanted interactions is kept below user-defined compatibility level. In addition it can be used to select optimal primer pairs for multiplexing from list of candidates. MultiPLX can be downloaded for local use or used online through a Graphical web-based interface.

TipMT / Tool for Identification of Primers for Multiple Taxa

Identifies and targets single sequence repeats (SSR) or orthologous/taxa-specific genes for genotyping using Multiplex PCR. TipMT is a web application to search and design primers for genotyping based on genomic data. This pipeline was applied to the genomes of four species of Leishmania (L. amazonensis, L. braziliensis, L. infantum and L. major) and validated by PCR using artificial genomic DNA mixtures of the Leishmania species as templates. TipMT can be applied to a broad spectrum of research topics including both molecular diagnostic and evolutionary studies.

MPprimer / Multiplex Polymerase primer

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A web app for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex polymerase chain reaction. MPprimer employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. MPprimer provides a virtual electrophotogram to help users choose the best primer set combination.