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dc.contributor.authorOu, Hong-Yu
dc.contributor.authorHe, Xinyi
dc.contributor.authorHarrison, Ewan M.
dc.contributor.authorKulasekara, Bridget R.
dc.contributor.authorThani, Ali Bin
dc.contributor.authorKadioglu, Aras
dc.contributor.authorHinton, Jay C. D.
dc.contributor.authorBarer, Michael R.
dc.contributor.authorDeng, Zixin
dc.contributor.authorRajakumar, Kumar
dc.contributor.authorLory, Stephen
dc.date.accessioned2011-07-01T16:24:32Z
dc.date.issued2007
dc.identifier.citationOu, Hong-Yu, Xinyi He, Ewan M. Harrison, Bridget R. Kulasekara, Ali Bin Thani, Aras Kadioglu, Stephen Lory, and et al. 2007. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Research 35: W97-W104.en_US
dc.identifier.issn0305-1048en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:4931361
dc.description.abstractMobilomeFINDER (http://mml.sjtu.edu.cn/MobilomeFINDER) is an interactive online tool that facilitates bacterial genomic island or ‘mobile genome’ (mobilome) discovery; it integrates the ArrayOme and tRNAcc software packages. ArrayOme utilizes a microarray-derived comparative genomic hybridization input data set to generate ‘inferred contigs’ produced by merging adjacent genes classified as ‘present’. Collectively these ‘fragments’ represent a hypothetical ‘microarray-visualized genome (MVG)’. ArrayOme permits recognition of discordances between physical genome and MVG sizes, thereby enabling identification of strains rich in microarray-elusive novel genes. Individual tRNAcc tools facilitate automated identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites and other integration hotspots in closely related sequenced genomes. Accessory tools facilitate design of hotspot-flanking primers for in silico and/or wet-science-based interrogation of cognate loci in unsequenced strains and analysis of islands for features suggestive of foreign origins; island-specific and genome-contextual features are tabulated and represented in schematic and graphical forms. To date we have used MobilomeFINDER to analyse several Enterobacteriaceae, Pseudomonas aeruginosa and Streptococcus suis genomes. MobilomeFINDER enables high-throughput island identification and characterization through increased exploitation of emerging sequence data and PCR-based profiling of unsequenced test strains; subsequent targeted yeast recombination-based capture permits full-length sequencing and detailed functional studies of novel genomic islands.en_US
dc.language.isoen_USen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofdoi:10.1093/nar/gkm380en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933208/pdf/en_US
dash.licenseLAA
dc.titleMobilomeFINDER: Web-Based Tools for In Silico and Experimental Discovery of Bacterial Genomic Islandsen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalNucleic Acids Researchen_US
dash.depositing.authorLory, Stephen
dc.date.available2011-07-01T16:24:32Z
dash.affiliation.otherHMS^Microbiology and Molecular Geneticsen_US
dc.identifier.doi10.1093/nar/gkm380*
dash.authorsorderedfalse
dash.contributor.affiliatedLory, Stephen


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