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Related Concept Videos

Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
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...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Updated: May 18, 2026

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
09:30

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

Gap detection for genome-scale constraint-based models.

J Paul Brooks1, William P Burns, Stephen S Fong

  • 1Center for the Study of Biological Complexity, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA 23284, USA ; Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA 23284, USA.

Advances in Bioinformatics
|September 22, 2012
PubMed
Summary
This summary is machine-generated.

FBA-Gap algorithm aids in building constraint-based metabolic models by suggesting plausible reaction additions. This method efficiently generates hypotheses for minimal media, improving model construction accuracy.

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Last Updated: May 18, 2026

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Area of Science:

  • Systems biology
  • Metabolic engineering
  • Computational biology

Background:

  • Constraint-based metabolic models are essential for system-wide cellular metabolism analysis.
  • Building accurate in silico models requires addressing challenges before flux balance analysis (FBA).

Purpose of the Study:

  • To present the FBA-Gap algorithm for constructing functional constraint-based metabolic models.
  • To demonstrate the algorithm's utility in generating minimal media hypotheses and improving model reconstruction.

Main Methods:

  • The FBA-Gap algorithm modifies existing reaction lists to enable biomass production via FBA.
  • It incorporates biologically plausible reactions and exchange reactions for model completion.

Main Results:

  • The algorithm successfully aided in creating a new model organism.
  • It generated hypotheses for minimal culture media for four existing models.
  • FBA-Gap proved more efficient and accurate than previous methods, adding fewer reactions.

Conclusions:

  • FBA-Gap is an effective tool for metabolic model construction and refinement.
  • The algorithm facilitates the generation of testable hypotheses for cellular metabolism and culture conditions.