IslandViewer: an Integrated Interface for Computational Identification and Visualization of Genomic Islands

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2009 Jan 20

PMID 19151094

Citations 253

Authors

Morgan G I Langille

Fiona S L Brinkman

Affiliations

Soon will be listed here.

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.

Availability: The IslandViewer web service is available at http://www.pathogenomics.sfu.ca/islandviewer and the source code is freely available under the GNU GPL license.

Citing Articles

Insights into the genomic and functional divergence of NAT gene family to serve microbial secondary metabolism.

Boukouvala S, Kontomina E, Olbasalis I, Patriarcheas D, Tzimotoudis D, Arvaniti K Sci Rep. 2024; 14(1):14905.

PMID: 38942826 PMC: 11213898. DOI: 10.1038/s41598-024-65342-4.

In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.

Kaur J, Verma H, Kaur J, Lata P, Dhingra G, Lal R Curr Microbiol. 2024; 81(8):233.

PMID: 38904756 DOI: 10.1007/s00284-024-03762-1.

Exploring the comparative genome of rice pathogen : unveiling virulence, fitness traits, and a potential type III secretion system effector.

Mannaa M, Lee D, Lee H, Han G, Kang M, Kim T Front Plant Sci. 2024; 15:1416253.

PMID: 38845849 PMC: 11153758. DOI: 10.3389/fpls.2024.1416253.

Bioinformatics and its role in the study of the evolution and probiotic potential of lactic acid bacteria.

Mendoza R, Kim S, Vasquez R, Hwang I, Park Y, Paik H Food Sci Biotechnol. 2023; 32(4):389-412.

PMID: 36911331 PMC: 9992694. DOI: 10.1007/s10068-022-01142-8.

Complete genome sequencing and comparative genomic analyses of a new spotted-fever strain B8.

He M, Zhang L, Hu H, Liu X, Zhang C, Xin Y Emerg Microbes Infect. 2022; 12(1):2153085.

PMID: 36440590 PMC: 9930820. DOI: 10.1080/22221751.2022.2153085.

References

Hacker J, Kaper J . Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol. 2000; 54:641-79. DOI: 10.1146/annurev.micro.54.1.641. View

Vernikos G, Parkhill J . Resolving the structural features of genomic islands: a machine learning approach. Genome Res. 2007; 18(2):331-42. PMC: 2203631. DOI: 10.1101/gr.7004508. View

Hsiao W, Ung K, Aeschliman D, Bryan J, Finlay B, Brinkman F . Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet. 2005; 1(5):e62. PMC: 1285063. DOI: 10.1371/journal.pgen.0010062. View

Ou H, He X, Harrison E, Kulasekara B, Thani A, Kadioglu A . MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res. 2007; 35(Web Server issue):W97-W104. PMC: 1933208. DOI: 10.1093/nar/gkm380. View

Ou H, Chen L, Lonnen J, Chaudhuri R, Thani A, Smith R . A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res. 2006; 34(1):e3. PMC: 1326021. DOI: 10.1093/nar/gnj005. View

Langille M, Hsiao W, Brinkman F . Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics. 2008; 9:329. PMC: 2518932. DOI: 10.1186/1471-2105-9-329. View

Rajan I, Aravamuthan S, Mande S . Identification of compositionally distinct regions in genomes using the centroid method. Bioinformatics. 2007; 23(20):2672-7. DOI: 10.1093/bioinformatics/btm405. View

Vernikos G, Parkhill J . Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics. 2006; 22(18):2196-203. DOI: 10.1093/bioinformatics/btl369. View

Tu Q, Ding D . Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis. FEMS Microbiol Lett. 2003; 221(2):269-75. DOI: 10.1016/S0378-1097(03)00204-0. View

10.

Karlin S . Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol. 2001; 9(7):335-43. DOI: 10.1016/s0966-842x(01)02079-0. View

11.

Dobrindt U, Hochhut B, Hentschel U, Hacker J . Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol. 2004; 2(5):414-24. DOI: 10.1038/nrmicro884. View

12.

Chiapello H, Bourgait I, Sourivong F, Heuclin G, Gendrault-Jacquemard A, Petit M . Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics. 2005; 6:171. PMC: 1187871. DOI: 10.1186/1471-2105-6-171. View

13.

Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke W . Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics. 2006; 7:142. PMC: 1489950. DOI: 10.1186/1471-2105-7-142. View

14.

Mantri Y, Williams K . Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res. 2003; 32(Database issue):D55-8. PMC: 308793. DOI: 10.1093/nar/gkh059. View