Degenerate primer design software tools | qPCR analysis

Produces degenerate primers for amplification and sequencing of short viral genomes. PriSM processes through three main steps for selecting and matching primers: make consensus, primer design and amplicon selection. This application can generate a panel of primer pairs that tile along the entire length of a viral genome. It can use a posteriori information of viral sequence databases to construct efficiently amplification primer pairs.

Begins conservational analysis for PCR primer design at the protein level, allowing the user to design consensus primers capable of detecting homologous coding sequences even when low-to-moderate sequence information is available. CEMAsuite also condenses the wealth of information associated with multiple sequence alignments and presents them in an intuitive manner, allowing the user to quickly and effectively address degenerate primer design considerations. The goal of CEMAsuite is to aid in the design of minimum-degeneracy primer sets which are robust enough for the assay at hand, while retaining as much specificity and product homology as possible.

Represents a program based on an algorithm called weighted randomized combination for solving the maximum coverage degenerate primer design problem. DegePrime preserves the correlation structure among nucleotides. This tool can design primers based on over a million sequences. It can be useful to substantially improve the taxonomic coverage of a popular primer pair for amplification of the region of bacterial.

Employs suffix array methods for efficient calculations on oligos 10-100 nt in length. PriMux is a software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups.

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.