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Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
2006
Computer applications in the biosciences : CABIOS
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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]
2017
bioRxiv
pre-print
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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
2008
Genome Research
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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
2018
Current Biology
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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
2020
Bioscience Reports
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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
2009
The ISME Journal
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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]
2021
bioRxiv
pre-print
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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
2011
Emerging Infectious Diseases
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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]
2016
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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