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Related Concept Videos

Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Types of Errors: Detection and Minimization01:12

Types of Errors: Detection and Minimization

Error is the deviation of the obtained result from the true, expected value or the estimated central value. Errors are expressed in absolute or relative terms.
Absolute error in a measurement is the numerical difference from the true or central value. Relative error is the ratio between absolute error and the true or central value, expressed as a percentage.
Errors can be classified by source, magnitude, and sign. There are three types of errors: systematic, random, and gross.
Systematic or...
Detection of Gross Error: The Q Test01:00

Detection of Gross Error: The Q Test

When one or more data points appear far from the rest of the data, there is a need to determine whether they are outliers and whether they should be eliminated from the data set to ensure an accurate representation of the measured value. In many cases, outliers arise from gross errors (or human errors) and do not accurately reflect the underlying phenomenon. In some cases, however, these apparent outliers reflect true phenomenological differences. In these cases, we can use statistical methods...

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Related Experiment Video

Updated: Jun 22, 2026

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR
14:14

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR

Published on: December 6, 2014

SHREC: a short-read error correction method.

Jan Schröder1, Heiko Schröder, Simon J Puglisi

  • 1Institut für Informatik, Christian-Albrecht-Universität Kiel, Herman-Rodewald-Strasse 3, 24118 Kiel, Germany. jasc@informatik.uni-kiel.de

Bioinformatics (Oxford, England)
|June 23, 2009
PubMed
Summary
This summary is machine-generated.

SHREC is a new algorithm for correcting errors in short-read sequencing data. It efficiently identifies and corrects errors, outperforming existing methods for de novo sequencing applications.

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Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
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Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
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Rare Event Detection Using Error-corrected DNA and RNA Sequencing

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Related Experiment Videos

Last Updated: Jun 22, 2026

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR
14:14

Simultaneous Quantification of T-Cell Receptor Excision Circles (TRECs) and K-Deleting Recombination Excision Circles (KRECs) by Real-time PCR

Published on: December 6, 2014

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Second-generation sequencing generates vast amounts of short reads.
  • Sequencing errors pose challenges for de novo sequencing.
  • Existing error correction methods are not optimized for short reads.

Purpose of the Study:

  • To develop a fast and accurate computational method for short-read error correction.
  • To address the limitations of current error correction tools for large datasets.

Main Methods:

  • Developed SHREC, an algorithm utilizing a generalized suffix trie.
  • Applied SHREC to simulated and real short-read sequencing data.

Main Results:

  • SHREC achieved >99% sensitivity and >96% specificity in identifying erroneous reads.
  • Error correction accuracy exceeded 80% for simulated and 88% for real data.
  • Demonstrated superior performance compared to previous approaches.

Conclusions:

  • SHREC offers a highly accurate and efficient solution for short-read error correction.
  • The open-source Java implementation can process millions of reads on standard hardware.