Nucleic Acids Research Advance Access first published online on May 30, 2007
This version published online on June 1, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm380
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MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands
1Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiaotong University, P. R. China, 2Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK, 3Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA, 4Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA and 5Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
*To whom correspondence should be addressed. Tel: +44 116 2231498; Fax: +44 116 2525030; Email: kr46{at}le.ac.uk *Correspondence may also be addressed to Zixin Deng. Tel: +86 21 62933404; Fax: +86 21 62932418; Email: zxdeng{at}sjtu.edu.cn
Received January 30, 2007. Revised April 22, 2007. Accepted April 30, 2007.
MobilomeFINDER (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.
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