IslandViewer: An integrated interface for computational identification and visualization of genomic islands

Morgan G.I. Langille; Fiona S.L. Brinkman

doi:10.1093/bioinformatics/btp030

IslandViewer: An integrated interface for computational identification and visualization of genomic islands

Morgan G.I. Langille, Fiona S.L. Brinkman

Résultat de recherche: Article › examen par les pairs

346 Citations (Scopus)

Résumé

Summary: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining precomputed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions.

Langue d'origine	English
Pages (de-à)	664-665
Nombre de pages	2
Journal	Bioinformatics
Volume	25
Numéro de publication	5
DOI	https://doi.org/10.1093/bioinformatics/btp030
Statut de publication	Published - mars 2009
Publié à l'externe	Oui

Note bibliographique

Funding Information:
M.G.I.L. also holds a MSFHR scholarship, while F.S.L.B. is a MSFHR Senior Scholar and CIHR New Investigator. Infrastructure support was also provided by Genome Canada/GenomeBC, SFU CTEF and IBM.

ASJC Scopus Subject Areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btp030

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abstract = "Summary: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining precomputed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions.",

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note = "Funding Information: M.G.I.L. also holds a MSFHR scholarship, while F.S.L.B. is a MSFHR Senior Scholar and CIHR New Investigator. Infrastructure support was also provided by Genome Canada/GenomeBC, SFU CTEF and IBM.",

year = "2009",

month = mar,

doi = "10.1093/bioinformatics/btp030",

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N2 - Summary: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining precomputed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions.

AB - Summary: Genomic islands (clusters of genes of probable horizontal origin; GIs) play a critical role in medically important adaptations of bacteria. Recently, several computational methods have been developed to predict GIs that utilize either sequence composition bias or comparative genomics approaches. IslandViewer is a web accessible application that provides the first user-friendly interface for obtaining precomputed GI predictions, or predictions from user-inputted sequence, using the most accurate methods for genomic island prediction: IslandPick, IslandPath-DIMOB and SIGI-HMM. The graphical interface allows easy viewing and downloading of island data in multiple formats, at both the chromosome and gene level, for method-specific, or overlapping, GI predictions.

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IslandViewer: An integrated interface for computational identification and visualization of genomic islands

Résumé

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ASJC Scopus Subject Areas

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