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Conventional primers design software tools | qPCR analysis

Conventional primer design software for PCR analysis.

Primer3
Desktop
Web

Primer3

Open-source software used for primer design, often in high-throughput genomics…

Open-source software used for primer design, often in high-throughput genomics applications.

Primer3Plus
Web

Primer3Plus

A web interface to the Primer3 primer design program as an enhanced alternative…

A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3.

QuantPrime
Desktop
Web

QuantPrime

Allows primer pair design in small- to large-scale real-time reverse…

Allows primer pair design in small- to large-scale real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) analyses. QuantPrime is a web application which offers design and…

swga
Desktop

swga

Identifies selective primer sets for a given target genome and background. swga…

Identifies selective primer sets for a given target genome and background. swga evaluates all potential primer sequences and forms sets of valid primers. It automatically calculates a variety of…

MSP-HTPrimer
Desktop

MSP-HTPrimer

Designs primers automatically on both genomic strands to increase the success…

Designs primers automatically on both genomic strands to increase the success rate. MSP-HTPrimer is an integrated, web-based, and high-throughput pipeline and has no limitation on the number and size…

PerlPrimer
Desktop

PerlPrimer

A free, open-source GUI application written in Perl that designs primers for…

A free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.

MRPrimerW
Web

MRPrimerW

A straightforward but powerful tool for designing high-quality primer pairs…

A straightforward but powerful tool for designing high-quality primer pairs that can be used simultaneously to detect multiple target genes in qPCR experiments. MRPrimerW overcomes the major…

Primer-BLAST
Web

Primer-BLAST

Helps users design target-specific primers. Primer-BLAST is a web application…

Helps users design target-specific primers. Primer-BLAST is a web application that offers flexibility to accommodate different primer design. It incorporates a global alignment mechanism and is…

FastPCR
Desktop
Web

FastPCR

Predicts primer location and polymerase chain reaction (PCR) product sequences…

Predicts primer location and polymerase chain reaction (PCR) product sequences from chromosome lists, whole genomes or circular DNA. FastPCR is an integrated tool that finds all possible primer pairs…

AutoPrime
Web

AutoPrime

Allows to rapidly design primers for real-time PCR measurement of eucaryotic…

Allows to rapidly design primers for real-time PCR measurement of eucaryotic expression.

PrimerZ
Web

PrimerZ

A web application dedicated primarily to primer design for genes and human SNPs.

A web application dedicated primarily to primer design for genes and human SNPs.

Primaclade
Web
Desktop

Primaclade

Designs minimally degenerate primers for comparative studies of multiple…

Designs minimally degenerate primers for comparative studies of multiple species. Primaclade is a web-based primer prediction application that provides a solution for researchers who want to design…

j-CODEHOP
Desktop

j-CODEHOP

Designs COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOPs) from…

Designs COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOPs) from amino acid sequence alignments. j-CODEHOP is a tool integrated into the whole genome pairwise and multiple alignment editor…

Edesign
Web
Desktop

Edesign

A design tool for PCR primers together with an internal probe for conducting…

A design tool for PCR primers together with an internal probe for conducting quantitative PCR and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for…

BatchPrimer3
Web

BatchPrimer3

A comprehensive web primer design program using Primer3 core program as a major…

A comprehensive web primer design program using Primer3 core program as a major primer design engine to design different types of PCR primers and sequencing primers in a high-through manner.

PrimerHunter
Web

PrimerHunter

A tool for selecting highly sensitive and specific primers for virus subtyping.

A tool for selecting highly sensitive and specific primers for virus subtyping.

PCRTiler
Desktop
Web

PCRTiler

Allows users to detect candidate primers for each sub-region. PCRTiler is…

Allows users to detect candidate primers for each sub-region. PCRTiler is composed of a webserver to automate the design of multiple specific primer pairs covering one or multiple genomic loci. It…

Amplicon
Desktop

Amplicon

A tool for designing PCR primers where groups of related DNA sequences can be…

A tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form.

MRPrimer
Desktop

MRPrimer

Designs all possible feasible and valid primer pairs for an entire DNA…

Designs all possible feasible and valid primer pairs for an entire DNA database. MRPrimer takes a DNA sequence database and a set of filtering constraints as input, and then, over seven steps, it…

miRprimer
Desktop

miRprimer

Designs primers for polymerase chain reaction (PCR) amplification of microRNAs.…

Designs primers for polymerase chain reaction (PCR) amplification of microRNAs. miRprimer generates a number of putative primers based on an interpretation of the guidelines for manual primer design…

Primers-4-Yeast
Web

Primers-4-Yeast

Allows primers to be designed in batches for S. cerevisiae gene-targeting…

Allows primers to be designed in batches for S. cerevisiae gene-targeting transformations, and for the validation of correct insertions. Primers-4-Yeast enables fast, automated, accurate primer…

PrimerDesign-M
Web

PrimerDesign-M

This tool was developed to meet the demands of primer design for highly…

This tool was developed to meet the demands of primer design for highly variable sets of aligned sequences. It includes design requirements for next-generation sequences (NGS) including 454…

JCVI Primer…
Desktop

JCVI Primer Designer

A fully integrated computational PCR primer design pipeline that plays a key…

A fully integrated computational PCR primer design pipeline that plays a key role in high-throughput directed sequencing pipeline.

PrecisePrimer
Web

PrecisePrimer

A web-based primer design software made to assist experimentalists in any…

A web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries.

RUCS
Web

RUCS Rapid identification of PCR primers for Unique Core Sequences

Eases the burden of Polymerase chain reaction (PCR) primer design. RUCS is a…

Eases the burden of Polymerase chain reaction (PCR) primer design. RUCS is a web application that allows users to (i) identify unique core sequences for a given dataset of positive and negative…

G T A T C G C T A
ThermoAlign
Desktop

ThermoAlign

Represents a genome-aware primer pair design algorithm. ThermoAlign is able to…

Represents a genome-aware primer pair design algorithm. ThermoAlign is able to use prior information on the locations of genomic variants during the selection of primer pairs. In order to design…

G T A T C G C T A
msatcommander
Desktop

msatcommander

Is designed to search for microsatellite arrays, design primers, and tag…

Is designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated,…

RExPrimer
Web

RExPrimer

An integrated graphical web-based application for primer design which was…

An integrated graphical web-based application for primer design which was written in Python language.

PrimerMapper
Desktop

PrimerMapper

Facilitates the design of robust primers from any number of inputted sequences.…

Facilitates the design of robust primers from any number of inputted sequences. PrimerMapper permits users to visualize each primer sequence map in a browser. It allows users to draw new primers in…

Prim-SNPing
Desktop

Prim-SNPing

Provides interactive, user-friendly and cost-effective primer design for SNP…

Provides interactive, user-friendly and cost-effective primer design for SNP genotyping.

keeSeek
Desktop

keeSeek

A command line tool for generating, for a given reference genome, a set of…

A command line tool for generating, for a given reference genome, a set of k-mers absent in that genome. The main differences with respect to previously developed tools for neverwords generation are…

STITCHER
Web

STITCHER

Provides a central resource for researchers conducting all types of overlapping…

Provides a central resource for researchers conducting all types of overlapping PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely…

SP-Designer
Desktop

SP-Designer

An open source program providing a user friendly tool for the design of…

An open source program providing a user friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

PrimerSeq
Desktop

PrimerSeq

Designs RT-PCR primers that evaluate alternative splicing events by…

Designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data.

PD5
Desktop

PD5

An open-source collection of classes and utilities, providing a complete…

An open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis.

GenomePRIDE
Desktop

GenomePRIDE

Designs polymerase chain reaction (PCR) primers or long oligos on an annotated…

Designs polymerase chain reaction (PCR) primers or long oligos on an annotated sequence. GenomePRIDE is a highly flexible and scalable software, for designing oligos/primers for large-scale projects.…

PrimerView
Desktop

PrimerView

Designs forward and reverse primers from multi-sequence datasets, and generates…

Designs forward and reverse primers from multi-sequence datasets, and generates graphical outputs that map the position and distribution of primers to the target sequence. This module operates from…

Gibthon
Desktop

Gibthon

Facilitates the design of primers to create overlaps in DNA. Gibthon is a…

Facilitates the design of primers to create overlaps in DNA. Gibthon is a collection of web based tools to facilitate the design of primers for Gibson Assembly. It offers an easy to use web based…

OLIGO
Desktop

OLIGO

Allows to design and analyze sequencing and polymerase chain reaction (PCR)…

Allows to design and analyze sequencing and polymerase chain reaction (PCR) primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons. OLIGO is a multi-functional…

ORFprimer
Desktop

ORFprimer

A package for automatical primer design. Protein sequences are typically…

A package for automatical primer design. Protein sequences are typically downloaded by simply specifying the GI identifier or accession number of the corresponding protein target. ORFprimer extracts…

PrimerProspecto…
Desktop

PrimerProspector

An extensible framework for primer design and analysis. PrimerProspector can be…

An extensible framework for primer design and analysis. PrimerProspector can be used for any nucleic acid sequences and allows users to design de novo primers based upon arbitrary multiple sequence…

PRISE2
Desktop

PRISE2 PRImer SElector 2

A software tool for designing sequence-selective PCR primers and probes. To…

A software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, it allows the user to specify a collection of target sequences that the primers are…

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.

PrimerIdent
Web

PrimerIdent

A web-based primer design tool for the specific amplification of individual…

A web-based primer design tool for the specific amplification of individual members of multigenic families across related species and also to evaluate the differential expression of isogenes for a…

PhiSiGns
Desktop
Web

PhiSiGns

Provides a convenient web interface that allows biologists to perform a dynamic…

Provides a convenient web interface that allows biologists to perform a dynamic search against selected phage genomes of interest, identify signature genes, generate sequence alignments, and design…

URPD
Web

URPD yoUR Primer Design

Provides specific primer design results. The pipeline design path makes it easy…

Provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter…

Blast Primer
Web

Blast Primer

Allows users to predict mouse gene. Blast Primer allows identification of…

Allows users to predict mouse gene. Blast Primer allows identification of real-time Polymerase chain reaction (PCR) primer candidates for cDNAs of interest for the deer mouse that can be used for…

PrimerServer
Web
Desktop

PrimerServer

Designs high-throughput specific primers. The workflow of PrimerServer consists…

Designs high-throughput specific primers. The workflow of PrimerServer consists of three steps: (i) primer design, primer specificity check, and data integration, (ii) sequences of candidate primer…

FlexGrePPS
Desktop

FlexGrePPS Flexible Greedy Peptide Pool Search

Provides a solution for proteomic compression. FlexGrePPS is an algorithm for…

Provides a solution for proteomic compression. FlexGrePPS is an algorithm for the construction of near optimal sets of degenerate peptide pools that lend themselves to rapid and economical screening…

eprimer32
Desktop

eprimer32

Pick Polymerase Chain Reaction (PCR) primers and hybridization oligos.…

Pick Polymerase Chain Reaction (PCR) primers and hybridization oligos. eprimer32 is an interface to the 'primer3' program (2.x series) from the Whitehead Institute. The Whitehead program…

skipseq
Desktop

skipseq

Reads and writes (return) sequences, skipping first few. skipseq is a variant…

Reads and writes (return) sequences, skipping first few. skipseq is a variant of the standard program for reading and writing sequences, seqret. It performs exactly the same function except that it…

eprimer3
Desktop

eprimer3

Picks PCR primers and hybridization oligos. eprimer3 is an interface to the…

Picks PCR primers and hybridization oligos. eprimer3 is an interface to the 'primer3' program from the Whitehead Institute. The Whitehead program must be set up and on the path in order for…

primersearch
Desktop

primersearch

Searches DNA sequences for matches with primer pairs. primersearch reads in…

Searches DNA sequences for matches with primer pairs. primersearch reads in primer pairs from an input file and searches them against DNA sequence(s) specified by the user. Each of the primers in a…

Beacon Designer
Desktop

Beacon Designer

Automates the design of real time primers and probes. Beacon Designer is used…

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…

AlleleID
Desktop

AlleleID

Addresses the challenges of bacterial identification, pathogen detection or…

Addresses the challenges of bacterial identification, pathogen detection or species identification. AlleleID is a comprehensive desktop tool to design species identification/cross species probes for…

PrimerQuest
Web

PrimerQuest

Provides extensive live design customization and can be used to design assays…

Provides extensive live design customization and can be used to design assays for species other than human, mouse, and rat. PrimerQuest design tool that enables customers to design primers and probes…

Pythia
Desktop

Pythia

A thermodynamically based PCR primer design program.

A thermodynamically based PCR primer design program.

BOSS
Desktop

BOSS Batch Oligo Selection Script

A batch primer selection program designed to select PCR oligos for gap closure…

A batch primer selection program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps.

SaskPrimerFS
Desktop

SaskPrimerFS

Designed to infer intronic regions of a target species and design for them by…

Designed to infer intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.

Primer Designer
Desktop

Primer Designer

This is a program to aid in designing of primers and creation of primer sheets.

This is a program to aid in designing of primers and creation of primer sheets.

VectorFriends
Desktop

VectorFriends

An integrated and user-friendly sequence analysis software tool for molecular…

An integrated and user-friendly sequence analysis software tool for molecular biologists. VectorFriends includes support for Isothermal assembly. With only a few clicks, Primer3 will pick the best…

Uniprime2
Web

Uniprime2 Universal primer design webservice

A web service which automatically designs large sets of universal primers by…

A web service which automatically designs large sets of universal primers by simply inputting a GeneID reference.

ConservedPrimer…
Desktop
Web

ConservedPrimers

Allows to design intron-flanking primers. ConservedPrimers is a high-throughput…

Allows to design intron-flanking primers. ConservedPrimers is a high-throughput pipeline that can be used for single nucleotide polymorphism (SNP) discovery, genetic variation assays and marker…

VizPrimer
Web

VizPrimer

A visualized web server for primer design.

A visualized web server for primer design.

PRIMEX
Web
Desktop

PRIMEX PRImer Match Extractor

Detects oligonucleotide sequences in whole genomes, allowing for mismatches.…

Detects oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries from client software and returns matches…

PTPan
Desktop

PTPan Position Tree Pan

A space-efficient indexing structure for approximate oligonucleotide string…

A space-efficient indexing structure for approximate oligonucleotide string matching in nucleic acid sequence data. Based on suffix trees, PTPan combines partitioning, truncation and a new suffix…

UniPrimer
Web

UniPrimer

Compares multiple primate sequences and designs primers for the conserved…

Compares multiple primate sequences and designs primers for the conserved sequences. UniPrimer is a web application that realizes searches for users about sequence with a pair of polymerase chain…

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