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IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis.
Dhillon, Bhavjinder K; Laird, Matthew R; Shay, Julie A; Winsor, Geoffrey L; Lo, Raymond; Nizam, Fazmin; Pereira, Sheldon K; Waglechner, Nicholas; McArthur, Andrew G; Langille, Morgan G I; Brinkman, Fiona S L.
Afiliación
  • Dhillon BK; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
  • Laird MR; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
  • Shay JA; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
  • Winsor GL; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
  • Lo R; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
  • Nizam F; M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
  • Pereira SK; M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
  • Waglechner N; M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
  • McArthur AG; M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada.
  • Langille MG; Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
  • Brinkman FS; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada brinkman@sfu.ca.
Nucleic Acids Res ; 43(W1): W104-8, 2015 Jul 01.
Article en En | MEDLINE | ID: mdl-25916842
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Genoma Bacteriano / Genoma Arqueal / Islas Genómicas Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2015 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Genoma Bacteriano / Genoma Arqueal / Islas Genómicas Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2015 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido