title: Identification of phage-induced genomic islands in the 13 Streptococcus pyogenes strains using genome barcodes.
abstract: With the revolutionary invention of the high-throughput sequencing technique, the production of bacterial genomes is significantly sped up. The in silico characterisation of genomic islands (GIs) in the pathogenic bacterium becomes increasingly needed, due to the time consumption and the high cost of the experimental techniques. A GI can be computationally detected through the DNA composition. Barcode, a dimension reduction and visualisation technique of genomic DNA composition, was recently applied to detect different DNA compositions effectively. In this work, we proposed a Barcode-based technique to detect Phage-induced Genomic Islands (PGIs) in the 13 completely sequenced strains of Streptococcus pyogenes. Our experimental results showed that the detected PGIs are highly consistent with the known GIs, the novel PGIs are promising candidates for the clinical diagnosis of S. pyogenes.
authors.forename: Chunbao
authors.initials: C
authors.lastname: Zhou
authors.forename: Jiaxin
authors.initials: J
authors.lastname: Wang
authors.forename: Yao
authors.initials: Y
authors.lastname: Wang
authors.forename: Yanchun
authors.initials: Y
authors.lastname: Liang
mesh_terms: D000465:Algorithms; D001435:Bacteriophages; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D058893:DNA Barcoding, Taxonomic; D016680:Genome, Bacterial; D044404:Genomic Islands; D015233:Models, Statistical; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012680:Sensitivity and Specificity; D013045:Species Specificity; D013297:Streptococcus pyogenes / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S