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Primer quality software tools | qPCR analysis

Primer quality software for PCR analysis.

MELTING
Web
Desktop

MELTING

Computes the enthalpy, the entropy and the melting temperature of the…

Computes the enthalpy, the entropy and the melting temperature of the helix-coil transitions for a nucleic acid duplex. MELTING uses approximate formulae or Nearest-Neighbor approaches. The software…

MFEprimer
Desktop

MFEprimer

Allows users to check primer specificity against genomic DNA and mRNA/cDNA…

Allows users to check primer specificity against genomic DNA and mRNA/cDNA sequence databases quickly and easily.

OligoCalc
Web

OligoCalc Oligonucleotide properties Calculator

A web-accessible, client-based computational engine for reporting DNA and RNA…

A web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties.

OligoAnalyzer
Web

OligoAnalyzer

Provides useful predictions of oligonucleotide properties under various…

Provides useful predictions of oligonucleotide properties under various experimental conditions. The OligoAnalyzer is the central calculator where various kinds of information about an…

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…

e-PCR
Web

e-PCR Electronic PCR

Identifies sequence tagged sites (STSs) within DNA sequences. e-PCR is a web…

Identifies sequence tagged sites (STSs) within DNA sequences. e-PCR is a web application which searches for sub-sequences that closely match the polymerase chain reaction (PCR) primers and have the…

dnaMATE
Web

dnaMATE

This server calculates a consensus melting temperature (Tm) for any given short…

This server calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) using a merged method that is based on three different thermodynamic tables.

AutoDimer
Web

AutoDimer

Developed to rapidly screen previously selected PCR primers for primer-dimer…

Developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions in short DNA oligomers.

pcrEfficiency
Web

pcrEfficiency

An open source tool which allows PCR efficiency prediction.

An open source tool which allows PCR efficiency prediction.

MIPE
Desktop

MIPE MIcrobiota Prior knowledge Explorer

Combines automated small subunit (SSU) primer evaluation with rRNA gene…

Combines automated small subunit (SSU) primer evaluation with rRNA gene extraction and classification for the analysis of shotgun metagenomic and metatranscriptomic datasets. MIPE is a metagenome…

PRaTo
Web

PRaTo Primer Rank Tool

A web-based tool that enables checking and ranking of primers pairs for their…

A web-based tool that enables checking and ranking of primers pairs for their attitude to perform optimally and reliably when used in qPCR experiments.

probeCheck
Web

probeCheck

Provides a freely accessible, central platform for rapid specificity and…

Provides a freely accessible, central platform for rapid specificity and coverage evaluations of probes and primers against the latest sequence collections of selected phylogenetic and functional…

Simulate_PCR
Desktop

Simulate_PCR

Software that can be run from the command line for high throughput applications…

Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as…

ecoPCR
Desktop

ecoPCR

Allows users to estimate Barcode primers quality. ecoPCR is an electronic…

Allows users to estimate Barcode primers quality. ecoPCR is an electronic Polymerase Chain Reaction (PCR) software which helps to compute barcode coverage and barcode specificity. It preserves the…

dan
Desktop

dan

Calculates nucleic acid melting temperature. dan calculates the percentage of…

Calculates nucleic acid melting temperature. dan calculates the percentage of G+C nucleotides for windows over a nucleic acid sequence and can plot it with the melting temperature. If a plot is not…

VisualOMP
Desktop

VisualOMP

Improves assay sensitivity by accurately predicting the secondary structure and…

Improves assay sensitivity by accurately predicting the secondary structure and locating the sites on the target that are most thermodynamically accessible.

GenomeTester
Web

GenomeTester

Tests whether PCR primers have excessive number of binding sites on template…

Tests whether PCR primers have excessive number of binding sites on template sequence and how many PCR products would be amplified from the template DNA and where are they located.

OligoEvaluator
Web

OligoEvaluator

An online oligonucleotide sequence calculator. OligoEvaluator is easy to use:…

An online oligonucleotide sequence calculator. OligoEvaluator is easy to use: register or login, select DNA or RNA, paste your sequence and click calculate. All reported properties are available for…

NetPrimer
Web

NetPrimer

Combines the latest primer analysis algorithms with a web-based interface…

Combines the latest primer analysis algorithms with a web-based interface allowing the user to analyze primers over the Internet.

ASePCR
Web

ASePCR

An efficient web-based application that emulates RT-PCR in various tissues.

An efficient web-based application that emulates RT-PCR in various tissues.

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