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Related Concept Videos

PCR01:32

PCR

Overview
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...
PCR - Polymerase Chain Reaction01:32

PCR - Polymerase Chain Reaction

Overview

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Related Experiment Video

Updated: May 21, 2026

Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies
09:00

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Published on: May 22, 2012

MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.

Wubin Qu1, Yang Zhou, Yanchun Zhang

  • 1Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center, Beijing 100850, China.

Nucleic Acids Research
|June 13, 2012
PubMed
Summary
This summary is machine-generated.

MFEprimer-2.0 is a free online tool for evaluating polymerase chain reaction (PCR) primer specificity. It uses a k-mer index and thermodynamics to quickly assess primer binding to DNA and RNA sequences.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • Primer specificity is crucial for accurate polymerase chain reaction (PCR) results.
  • Existing methods for evaluating primer specificity can be time-consuming and complex.

Purpose of the Study:

  • To introduce MFEprimer-2.0, a user-friendly web server for assessing PCR primer specificity.
  • To provide a rapid and reliable method for evaluating primer binding to genomic DNA and RNA sequences.

Main Methods:

  • MFEprimer-2.0 employs a k-mer index algorithm for accelerated identification of primer binding sites.
  • Thermodynamic principles are utilized to evaluate the binding stability between primers and DNA templates.
  • The server analyzes amplicon characteristics including sequence, melting temperature, and size.

Main Results:

  • MFEprimer-2.0 provides a user-friendly interface for easy interpretation of primer specificity.
  • The tool supports analysis of degenerate and multiple PCR primers.
  • Comprehensive databases are integrated, with options for custom database support.

Conclusions:

  • MFEprimer-2.0 facilitates efficient and accurate evaluation of PCR primer specificity.
  • The server aids researchers in drawing conclusions about primer suitability for molecular biology applications.
  • MFEprimer-2.0 is freely accessible online and offers open-source versions for local use.