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Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands

Georgios S. Vernikos, Julian Parkhill
2006 Computer applications in the biosciences : CABIOS  
order motif methods predicting not only the already characterized Salmonella Pathogenicity Islands (SPI-1 to SPI-10) but also three novel SPIs (SPI-15, SPI-16, SPI-17) and other HGT events.  ...  Results: We introduce a novel computational method, Interpolated Variable Order Motifs (IVOMs), which exploits compositional biases using variable order motif distributions and captures more reliably the  ...  the BioJava source code and comments on the manuscript, David Carter for his valuable suggestions on the implementation of the HMM theory and Tim Carver for his helpful suggestions and technical support  ... 
doi:10.1093/bioinformatics/btl369 pmid:16837528 fatcat:xfa5figccjgpvaya2ldexsezey

A target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA in environmental and clinical specimens [article]

Enrique Zozaya-Valdes, Jessica L. Porter, John Coventry, Janet A.M. Fyfe, Glen P. Carter, Anders Goncalves da Silva, Torsten Seemann, Paul D.R. Johnson, Andrew J. Stewardson, Ivan Bastian, Sally A. Roberts, Benjamin P. Howden (+2 others)
2017 bioRxiv   pre-print
We targeted one of these regions and developed a TaqMan qPCR assay for M. chimaera with a detection limit of 10 CFU in whole blood.  ...  In vitro screening against DNA extracted from 40 other mycobacteria and 22 bacterial species from 21 diverse genera confirmed in silico predicted specificity for M. chimaera.  ...  We thank submitting health-care facilities and laboratories for providing water  ... 
doi:10.1101/105213 fatcat:c5oyqdmeozbgjfl5v7b3wjvqqq

Resolving the structural features of genomic islands: A machine learning approach

G. S. Vernikos, J. Parkhill
2008 Genome Research  
Large inserts of horizontally acquired DNA that contain functionally related genes with limited phylogenetic distribution are often referred to as genomic islands (GIs), and structural definitions of these  ...  Although a large number of mobile elements fall well within the GI definition, there are several concerns about the structural consensus for GIs: The current GI definition was put forward 10 yr ago when  ...  Thomson and Matthew Holden for discussion on aspects of the comparative analysis.  ... 
doi:10.1101/gr.7004508 pmid:18071028 pmcid:PMC2203631 fatcat:rpiyfvzg2vgeniu7xzfvcdgyku

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

Zhemin Zhou, Inge Lundstrøm, Alicia Tran-Dien, Sebastián Duchêne, Nabil-Fareed Alikhan, Martin J. Sergeant, Gemma Langridge, Anna K. Fotakis, Satheesh Nair, Hans K. Stenøien, Stian S. Hamre, Sherwood Casjens (+7 others)
2018 Current Biology  
The authors declare no competing interests.  ...  Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22, 2196-2203. 116.  ...  Some core genes are universally present in the Para C lineage plus Birkenhead even though they belong to mobile genetic elements that are variably present in other Salmonella, e.g., the pathogenicity islands  ... 
doi:10.1016/j.cub.2018.05.058 pmid:30033331 pmcid:PMC6089836 fatcat:dynvxrc4xbcjtbwodeqqebuwv4

Genomic Islands and the Evolution of Livestock-Associated Staphylococcus aureus genomes

Rao Relangi Tulasi, Shivani Sharma, Natesan Sivakumar, Kannan Jayakumar
2020 Bioscience Reports  
Genomic Islands (GIs) are commonly believed to be relics of horizontal transfer and associated with specific metabolic capacities, including virulence of the strain.  ...  Methods: Genomic Islands were predicted with two methods namely, Ensemble algorithm for Genomic Island Detection (EGID) tool, and Seq word Sniffer script.  ...  Vernikos GS, Parkhill J. (2006) Interpolated variable order motifs for identification of 421 horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.  ... 
doi:10.1042/bsr20202287 pmid:33185245 pmcid:PMC7689654 fatcat:d252mua26zdlffd3cteejchdr4

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

Michelle A Allen, Federico M Lauro, Timothy J Williams, Dominic Burg, Khawar S Siddiqui, Davide De Francisci, Kevin W Y Chong, Oliver Pilak, Hwee H Chew, Matthew Z De Maere, Lily Ting, Marilyn Katrib (+12 others)
2009 The ISME Journal  
The genome of M. burtonii was sequenced at the Joint Genome Institute (JGI) using a combination of 3 kb, 8 kb and 40 kb DNA libraries.  ...  Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the  ...  Nucleic Acids Res. 33: 922-933 Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.  ... 
doi:10.1038/ismej.2009.45 pmid:19404327 fatcat:7fe7yj7jtbgfrprp4q2r7kw52u

Metapopulation Structure of Diatom-associated Marine Bacteria [article]

Liping Qu, Xiaoyuan Feng, Yuerong Chen, Lingyu Li, Xiaojun Wang, Zhong Hu, Hui Wang, Haiwei Luo
2021 bioRxiv   pre-print
Six of these populations are members of Sulfitobacter, arguably the most prevalent bacteria associated with marine diatoms.  ...  These bacteria constitute eight genetically monomorphic populations of the globally abundant Roseobacter group.  ...  Parkhill, Interpolated variable order motifs for identification of 489 horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. 490 Bioinformatics 22, 2196-2203 (2006). 491 74. D.  ... 
doi:10.1101/2021.03.10.434754 fatcat:kq3mxfbmrfapjeyem5kyuke32m

Molecular Epidemiology of Fonsecaea Species

Mohammad Javad Najafzadeh
2011 Emerging Infectious Diseases  
Sequencing-based approaches for pathogen identification are being applied to pneumonia patients (3).  ...  Moon is an assistant professor at the Seoul National University Hospital. His primary research interests include metagenomics analysis for pathogen identification from clinical samples. Dr.  ...  a relatively short sequencing time would be sufficient for pathogen identification.  ... 
doi:10.3201/1703.100555 fatcat:4bb26n73mfah7a3ujwyzyyeudy

Novel strategies in the approach to primary immunodeficiencies to discover new pathogenic mechanisms and complex clinical phenotypes [article]

Giuliana Giardino
2016
Onlus (www.incontinentiapigmenti.it) for contributing to this research study. Disclosure Statement: The authors declare no financial conflict of interest.  ...  RW performed the statistical analyses. AJ, NG and SS supervised the writing of the manuscript. Conflict of interest The authors declare no conflict of interest.  ...  The NGS approach represent a very powerful tool for the rapid gene identification of typical phenotypes, for the identification of new genetic defects associated to classical phenotypes, for the definitions  ... 
doi:10.6093/unina/fedoa/10894 fatcat:czlbdun3bzfopd3l6irxfhdp5a