IslandViewer 3: More flexible, interactive genomic island discovery, visualization and analysis

Bhavjinder K. Dhillon; Matthew R. Laird; Julie A. Shay; Geoffrey L. Winsor; Raymond Lo; Fazmin Nizam; Sheldon K. Pereira; Nicholas Waglechner; Andrew G. McArthur; Morgan G.I. Langille; Fiona S.L. Brinkman

doi:10.1093/nar/gkv401

IslandViewer 3: More flexible, interactive genomic island discovery, visualization and analysis

Bhavjinder K. Dhillon, Matthew R. Laird, Julie A. Shay, Geoffrey L. Winsor, Raymond Lo, Fazmin Nizam, Sheldon K. Pereira, Nicholas Waglechner, Andrew G. McArthur, Morgan G.I. Langille, Fiona S.L. Brinkman

Medicine

Résultat de recherche: Article › examen par les pairs

248 Citations (Scopus)

Résumé

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.

Langue d'origine	English
Pages (de-à)	W104-W108
Journal	Nucleic Acids Research
Volume	43
Numéro de publication	W1
DOI	https://doi.org/10.1093/nar/gkv401
Statut de publication	Published - 2015

Note bibliographique

Funding Information:
Genome British Columbia/Genome Canada; Simon Fraser University Community Trust Endowment Fund; Canadian Institutes for Health Research Bioinformatics Training Program scholarship [to B.K.D.]; Cystic Fibrosis Canada scholarship [to J.A.S.]; McMaster Work Programs [to S.K.P.]; CIHR Doctoral research award [to N.W.]; Cisco Systems Canada Research Chair in Bioinformatics [to A.G.M.]. Funding for open access charge: Genome Canada.

Funding Information:
Genome British Columbia/Genome Canada; Simon Fraser University Community Trust Endowment Fund; Canadian Institutes for Health Research Bioinformatics Training Program scholarship [to B.K.D.]; Cystic Fibrosis Canada scholarship [to J.A.S.]; McMaster Work Programs [to S.K.P.]; CIHR Doctoral research award [to N.W.]; Cisco Systems Canada Research Chair in Bioinformatics [to A.G.M.]. Funding for open access charge: Genome Canada. Conflict of interest statement. None declared.

Publisher Copyright:
© 2015 The Author(s).

ASJC Scopus Subject Areas

Genetics

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10.1093/nar/gkv401

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@article{3224fa3a59ff45c1a5dd205232c9fda9,

title = "IslandViewer 3: More flexible, interactive genomic island discovery, visualization and analysis",

abstract = "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.",

author = "Dhillon, {Bhavjinder K.} and Laird, {Matthew R.} and Shay, {Julie A.} and Winsor, {Geoffrey L.} and Raymond Lo and Fazmin Nizam and Pereira, {Sheldon K.} and Nicholas Waglechner and McArthur, {Andrew G.} and Langille, {Morgan G.I.} and Brinkman, {Fiona S.L.}",

note = "Funding Information: Genome British Columbia/Genome Canada; Simon Fraser University Community Trust Endowment Fund; Canadian Institutes for Health Research Bioinformatics Training Program scholarship [to B.K.D.]; Cystic Fibrosis Canada scholarship [to J.A.S.]; McMaster Work Programs [to S.K.P.]; CIHR Doctoral research award [to N.W.]; Cisco Systems Canada Research Chair in Bioinformatics [to A.G.M.]. Funding for open access charge: Genome Canada. Funding Information: Genome British Columbia/Genome Canada; Simon Fraser University Community Trust Endowment Fund; Canadian Institutes for Health Research Bioinformatics Training Program scholarship [to B.K.D.]; Cystic Fibrosis Canada scholarship [to J.A.S.]; McMaster Work Programs [to S.K.P.]; CIHR Doctoral research award [to N.W.]; Cisco Systems Canada Research Chair in Bioinformatics [to A.G.M.]. Funding for open access charge: Genome Canada. Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} 2015 The Author(s).",

year = "2015",

doi = "10.1093/nar/gkv401",

language = "English",

volume = "43",

pages = "W104--W108",

journal = "Nucleic Acids Research",

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T2 - More flexible, interactive genomic island discovery, visualization and analysis

AU - Dhillon, Bhavjinder K.

AU - Laird, Matthew R.

AU - Shay, Julie A.

AU - Winsor, Geoffrey L.

AU - Lo, Raymond

AU - Nizam, Fazmin

AU - Pereira, Sheldon K.

AU - Waglechner, Nicholas

AU - McArthur, Andrew G.

AU - Langille, Morgan G.I.

AU - Brinkman, Fiona S.L.

N1 - Funding Information: Genome British Columbia/Genome Canada; Simon Fraser University Community Trust Endowment Fund; Canadian Institutes for Health Research Bioinformatics Training Program scholarship [to B.K.D.]; Cystic Fibrosis Canada scholarship [to J.A.S.]; McMaster Work Programs [to S.K.P.]; CIHR Doctoral research award [to N.W.]; Cisco Systems Canada Research Chair in Bioinformatics [to A.G.M.]. Funding for open access charge: Genome Canada. Funding Information: Genome British Columbia/Genome Canada; Simon Fraser University Community Trust Endowment Fund; Canadian Institutes for Health Research Bioinformatics Training Program scholarship [to B.K.D.]; Cystic Fibrosis Canada scholarship [to J.A.S.]; McMaster Work Programs [to S.K.P.]; CIHR Doctoral research award [to N.W.]; Cisco Systems Canada Research Chair in Bioinformatics [to A.G.M.]. Funding for open access charge: Genome Canada. Conflict of interest statement. None declared. Publisher Copyright: © 2015 The Author(s).

PY - 2015

Y1 - 2015

N2 - 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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IslandViewer 3: More flexible, interactive genomic island discovery, visualization and analysis

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