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Related Concept Videos

Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
Mismatch Repair01:36

Mismatch Repair

Overview
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Mismatch Repair01:36

Mismatch Repair

Overview

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Updated: Jun 24, 2026

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
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Metabolic pathfinding using RPAIR annotation.

Karoline Faust1, Didier Croes, Jacques van Helden

  • 1Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium. kfaust@ulb.ac.be

Journal of Molecular Biology
|March 14, 2009
PubMed
Summary
This summary is machine-generated.

Incorporating KEGG reactant pair data into metabolic networks significantly improves pathway inference accuracy. This approach effectively penalizes highly connected metabolites, leading to more reliable metabolic reconstruction in various organisms.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Metabolic Network Analysis

Background:

  • Metabolic databases represent biochemical reactions as networks, crucial for inferring metabolic pathways.
  • Pool metabolites create shortcuts, complicating accurate pathway reconstruction.
  • KEGG provides reaction decompositions into reactant pairs (RPAIR) categorizing metabolite roles.

Purpose of the Study:

  • To evaluate the impact of KEGG RPAIR data on metabolic pathway inference.
  • To optimize metabolic network construction parameters for improved pathfinding.
  • To assess the accuracy of pathway recovery using different network configurations.

Main Methods:

  • Constructed metabolic networks by mapping reactions and RPAIR data.
  • Applied various weighting schemes and metabolite filtering strategies.
  • Tested 104 parameter combinations on 55 reference pathways from E. coli, S. cerevisiae, and humans.

Main Results:

  • The optimal network integrated KEGG RPAIR data with a weighting scheme penalizing highly connected compounds.
  • This approach achieved high accuracy in recovering reference pathways: 93% for E. coli, 66% for S. cerevisiae, and 70% for humans.
  • The pathfinding approach is available within the Network Analysis Tools.

Conclusions:

  • KEGG RPAIR data significantly enhances the accuracy of metabolic pathway inference.
  • Optimized metabolic network construction, including RPAIR data and metabolite weighting, is key for reliable pathfinding.
  • The developed method provides a robust tool for metabolic reconstruction and analysis.