Multiplex primer design software tools | Quantitative PCR data analysis
Multiplex polymerase chain reaction (PCR) is a particular application of PCR where several different DNA sequences are amplified simultaneously. This technique requires careful and optimized design of primer, as multiple primer pairs are used in the same reaction. Multiplex PCR can be used for targeted resequencing as an alternative to whole-genome or whole-exome sequencing. Multiplex primer software tools are used for optimal design and selection of primers and amplicons.
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.
Automates the design of real time primers and probes. Beacon Designer is used by molecular biologists worldwide to design successful real time polymerase chain reaction (PCR) assays. It saves the time and the money involved in failed experiments. It is a flexible solution to real-time primer and probe design needs and pays for itself many times over. In addition to locating the primer anywhere on the gene of interest, Beacon Designer can design primers across exon-exon or exon-intron junctions.
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.
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.
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.
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.