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Degenerate primer design software tools | qPCR analysis

A PCR primer sequence is called degenerate if some of its positions have several possible bases. Designed degenerate primers unlike conventional primers are superior in matching and amplification of large number of genes, from related gene families.

HYDEN
Desktop

HYDEN HighlY DEgeNerate primers

A program for designing pairs of degenerate primers for a given set of DNA…

A program for designing pairs of degenerate primers for a given set of DNA sequences. We report on the success of the program in an experimental scheme for identifying all human olfactory receptor…

CEMAsuite
Desktop

CEMAsuite Codon-Equivalent Multiple Alignment suite

Begins conservational analysis for PCR primer design at the protein level,…

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…

DegePrime
Desktop

DegePrime

Represents a program based on an algorithm called weighted randomized…

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…

CODEHOP
Web

CODEHOP COnsensus-DEgenerate Hybrid Oligonucleotide Primers

Designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence…

Designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments. CODEHOP is suited for cases where the protein sequences are distant from each other and degenerate primers…

Gemi
Desktop

Gemi

Fast, automated and user-friendly tool to design polymerase chain reaction…

Fast, automated and user-friendly tool to design polymerase chain reaction (PCR) primers.

PriMux
Desktop

PriMux

Employs suffix array methods for efficient calculations on oligos 10-100 nt in…

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…

FAS-DPD
Desktop

FAS-DPD Family-Specific Degenerate Primer Design

A package to design degenerate primers for PCR. FAS-DPD is very strict in the…

A package to design degenerate primers for PCR. FAS-DPD is very strict in the search of conserved regions and minimizes the amount of degeneracy incorporated at this end. The software is designed to…

dprimer
Desktop

dprimer

A command line utility for designing degenerate PCR primers against multiple,…

A command line utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

GeneFisher2
Web

GeneFisher2

Allows to design degenerate primers. GeneFisher2 is a web-based program that…

Allows to design degenerate primers. GeneFisher2 is a web-based program that helps user to find primers for degenerated sequences. The software incorporates BatCons2 which allows to calculate…

DPPrimer
Web

DPPrimer Degenerate PCR Primer

It was designed to predict primers for PCR amplification of homologous gene…

It was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species.

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