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Related Concept Videos

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...
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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.
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...

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Related Experiment Video

Updated: Jun 28, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Matching curated genome databases: a non trivial task.

Stéphane Descorps-Declère1, Matthieu Barba, Bernard Labedan

  • 1Institut de Génétique et Microbiologie, Université Paris Sud XI, CNRS UMR 8621, Bât, 400, 91405 Orsay Cedex, France. stephane.descorps-declere@igmors.u-psud.fr

BMC Genomics
|October 28, 2008
PubMed
Summary
This summary is machine-generated.

CorBank efficiently cross-references protein identifiers between genome databases, revealing significant annotation differences. This tool highlights discrepancies in RefSeq and Genome Reviews, aiding genomic data consistency.

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

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Last Updated: Jun 28, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

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Published on: August 15, 2019

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Independent genome curation by NCBI (RefSeq) and EBI (Genome Reviews) aims to improve annotation quality.
  • Uncoordinated curation efforts lead to challenges in mapping protein identifiers and structural annotation discrepancies.
  • Existing databanks (GenBank/EMBL/DDBJ) contain non-standard annotations necessitating curated versions.

Purpose of the Study:

  • To develop a program (CorBank) for cross-referencing protein identifiers across different genome databases.
  • To identify and quantify differences in structural annotations between independently curated genome versions.
  • To facilitate the retrieval of cross-references between major genomic databases.

Main Methods:

  • Implementation of CorBank, a program designed for cross-referencing protein identifiers irrespective of sequence identity.
  • Analysis of 641 complete genomes to compare RefSeq and Genome Reviews versions.
  • Utilizing CorBank to detect differences in coding sequences (CDS) and the number of CDS.

Main Results:

  • CorBank successfully cross-references approximately 98% of 1,983,258 amino acid sequences.
  • Significant annotation differences were found in 50 out of 641 analyzed complete genomes between RefSeq and Genome Reviews.
  • Discrepancies include variations in CDS and total CDS counts, indicating divergence in independent curation.

Conclusions:

  • CorBank effectively detects numerous differences between RefSeq and Genome Reviews curated genomes.
  • The study suggests improved communication between genome database curators to reduce annotation divergence.
  • Standardization and shared viewpoints in genome annotation are recommended for enhanced data consistency.