Abstract
Background: The non-conserved accessory genome of bacteria can be associated with important adaptive characteristics that can contribute to niche specificity or pathogenicity of strains. High degrees of structural and compositional diversity in genomic islands and other elements of the accessory genome can complicate characterization of accessory genome contents among populations of strains. Methods for easily and effectively defining the distributions of discrete elements of the accessory genome among bacterial strains in a population are needed to explore the relationships between the flexible genome and bacterial adaptive traits. Results: We have developed the open-source software package ClustAGE. This program, written in Perl, uses BLAST to cluster nucleotide accessory genomic elements from the genomes of multiple bacterial strains and to identify their distribution within the study population. The program output can be used in combination with strain phenotype data or other characteristics to detect associations. Optional graphical output is available for visualizing accessory genome gene content and distribution patterns. The capabilities of the software are demonstrated on a collection of 14 Pseudomonas aeruginosa genome sequences. Conclusions: The ClustAGE software and utilities are effective for identifying characteristics and distributions of accessory genomic elements among groups of bacterial genomes. The ability to easily and effectively characterize the accessory genome of a sequence collection may provide a better understanding of the accessory genome's contribution to a species' adaptation and pathogenesis. The ClustAGE source code can be downloaded from https://clustage.sourceforge.ioand a limited web-based implementation is available at http://vfsmspineagent.fsm.northwestern.edu/cgi-bin/clustage.cgi.
Original language | English (US) |
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Article number | 150 |
Journal | BMC bioinformatics |
Volume | 19 |
Issue number | 1 |
DOIs | |
State | Published - Apr 20 2018 |
Funding
Keywords
- Accessory genome
- Bacteria
- Comparative genomics
- Flexible genome
ASJC Scopus subject areas
- Structural Biology
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Applied Mathematics
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Additional file 3: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements
Ozer, E. A. (Creator), figshare, 2018
DOI: 10.6084/m9.figshare.6168476, https://springernature.figshare.com/articles/Additional_file_3_of_ClustAGE_a_tool_for_clustering_and_distribution_analysis_of_bacterial_accessory_genomic_elements/6168476
Dataset
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Additional file 1: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements
Ozer, E. A. (Creator), figshare, 2018
DOI: 10.6084/m9.figshare.6168449, https://springernature.figshare.com/articles/Additional_file_1_of_ClustAGE_a_tool_for_clustering_and_distribution_analysis_of_bacterial_accessory_genomic_elements/6168449
Dataset
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Additional file 6: of ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements
Ozer, E. A. (Creator), figshare, 2018
DOI: 10.6084/m9.figshare.6168518, https://springernature.figshare.com/articles/Additional_file_6_of_ClustAGE_a_tool_for_clustering_and_distribution_analysis_of_bacterial_accessory_genomic_elements/6168518
Dataset