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.
Allows users to design target-specific primers for real-time PCR (qPCR) experiments. Primer Express is designed for quantifying the gene expression and discriminating single nucleotide polymorphism (SNP). It does not require any specific computer program to run and can be installed with a normal configuration on different types of computer.
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.
Permits users to manage, test and design primers for polymerase chain reaction (PCR). AmplifX is an application developed to seek in a collection of primers those which can be used to amplify a fragment into a target sequence to design strategies to screen recombinant clones by PCR. It can also design new primers. Some information are associated with each primer, some automatically computed by the software and other are given by the user.
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.
Permits users to design oligos for multiplex assays, facilitating amplification of multiple targets in a single reaction vessel. PrimerPlex is an application that designs optimal multiplex primer sets under uniform reaction conditions, for over 100 sequences. To ensure the specificity of the primers, they can be searched in BLAST from any of the genomic databases available at the NCBI.