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Cis-regulatory Sequences

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Updated: Jun 18, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics.

Valérian Lupo^1,2, Mick Van Vlierberghe¹, Hervé Vanderschuren³

¹InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium.

Frontiers in Microbiology

|November 8, 2021

Summary

This summary is machine-generated.

Contaminating sequences in bacterial genomes are a major concern. Using multiple detection tools, like CheckM and Physeter, is crucial for accurate contamination assessment in public databases.

Keywords:

NCBI RefSeq assembly contamination databases genomes phylogenomics sequencing

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Last Updated: Jun 18, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

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Published on: August 25, 2018

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics
Microbial Ecology

Background:

Contaminating sequences in public genome databases pose a significant challenge.
Existing detection tools use diverse algorithms, leading to variable contamination estimates.
Reliance on single detection methods risks systematic errors in genomic studies.

Purpose of the Study:

To assess bacterial genome contamination in the NCBI RefSeq database using orthogonal methods.
To compare the performance of CheckM and the Physeter tool.
To highlight the necessity of employing multiple contamination detection strategies.

Main Methods:

Applied CheckM, a popular gene marker-based tool, to RefSeq bacterial genomes.
Utilized Physeter, a genome-wide method with a k-folds algorithm, for complementary analysis.
Compared results from both methods to identify discrepancies and missed contaminants.

Main Results:

CheckM produced dubious results for 12,326 bacterial genomes, limiting its applicability.
Physeter identified 239 contaminated genomes missed by CheckM.
Demonstrated CheckM's limitations across diverse bacterial groups.

Conclusions:

Using multiple orthogonal methods is essential for accurate genome contamination assessment.
The Physeter tool offers an improved approach to minimize inaccurate estimates, especially with contaminated reference databases.
Emphasizes the need for robust validation of genomic data integrity.