Related Experiment Video
Updated: Mar 14, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
SNP synteny analysis of Staphylococcus aureus and Pseudomonas aeruginosa population genomics
Patricia Morán Losada1, Burkhard Tümmler1,2
1Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Hannover D-30625, Germany.
Abstract:
Genomic sequence diversity of a bacterial species mainly results from the frequency distribution of single nucleotide polymorphisms (SNPs). Here we report on an SNP matrix-based binary algorithm to determine the intraclonal or interclonal genomic diversity by the number of shared sequential SNPs, the so-called SNP synteny or haplotype. All SNP positions and the frequency and length distribution of haplotypes are determined from pairwise alignment of completely sequenced genomes. This metric is invariant regarding the reference genome chosen. Information is obtained about the size of haplotypes, genomic gradients of recombination frequency, relatedness of strains and population composition of a taxon or clonal populations. The approach is illustrated with whole genome data sets of Staphylococcus aureus and Pseudomonas aeruginosa strains.
Related Concept Videos
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Single Nucleotide Polymorphisms-SNPs
Modern Molecular Taxonomy
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

