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. It then distributes primer pairs to groups for keeping the strength of unwanted interactions below user-defined compatibility level. In addition, it can be used to select optimal primer pairs for multiplexing from list of candidates.
Calculates covariance scores for constrained regions of background conservation. McBASC can be utilized as a covarying or highly conserved filter. This software gives an equally high score to conserved or covarying alignments and allows, without a reduction in score, substitution of conserved pairs of residues for covarying ones.
Automates the selection of polymerase chain reaction (PCR) amplicons in the least conserved regions within a group of genes. SPADS works on the genomic sequence and takes into account the intron-exon gene structure. It is able to process eukaryotic gene models. This tool performs in designing unique gene sequence tags (GSTs) from the annotated genomes of two model organisms, Arabidopsis and yeast.
Designs all possible polymerase chain reaction (PCR) primer pairs and oligos, followed by filtering for single nucleotide polymorphisms (SNPs) loci and repeat regions. MSRE-HTPrimer simplifies the design of primer pairs for epigenetic and genomic target validation studies. It can perform the design for hundreds to thousands of target sequences in a single run. This software annotates all resulting primer pairs extensively by adding genetic and epigenetic information.
Analyses and evaluates multiplex pyrosequencing results. MultiPSQ complements the analysis capabilities of the Qiagen pyrosequencing platform. This method classifies samples based on the similarity of their pyrosequencing fingerprints to theoretical fingerprints generated from known sequences. It is applicable to any problem where samples need to be classified based on nucleic acid sequences.
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.
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.
Designs multiplex polymerase chain reaction (PCR) experiments suitable for next-generation targeted resequencing. MPD allows an iterative design approach where initially stringent conditions and subsequently loosened to maximize the number of high-quality primers that are as close to the initial design criteria as biologically feasible. This application can be quickly retooled to enable shift in targeted genes as new genetic evidence emerges.
Scans automatically target DNA sequences and designs primers in regions of low degeneracy that are free of secondary structures (hairpins, dimers and false priming sites). Primer Premier searches for optimal polymerase chain reaction (PCR), multiplex and single nucleotide polymorphism (SNP) genotyping primers via a nearest neighbor algorithm. It supports multiplex assays and can automatically describe BLAST search results.
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.
Furnishes methods to design, evaluate, and compare primer sets for multiplex polymerase chain reaction (PCR). openPrimerR includes a primer design function that produces novel primer sets by solving a set cover problem to maximize the number of covered template sequences with the smallest possible set of primers. It provides features to assess existing primer sets according to their coverage and fulfilment of constraints on PCR-relevant physicochemical properties. A self-contained Docker image of the software is available.