Nucleic Acids Research Advance Access originally published online on May 30, 2007
Nucleic Acids Research 2007 35(Web Server issue):W97-W104; doi:10.1093/nar/gkm380
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W97-W104
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. J. van Aartsen The Klebsiella pheV tRNA locus: a hotspot for integration of alien genomic islands Bioscience Horizons, March 1, 2008; 1(1): 51 - 60. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H.-Y. Ou, C. T. S. Ju, K.-L. Thong, N. Ahmad, Z. Deng, M. R. Barer, and K. Rajakumar Translational Genomics to Develop a Salmonella enterica Serovar Paratyphi A Multiplex Polymerase Chain Reaction Assay J. Mol. Diagn., November 1, 2007; 9(5): 624 - 630. [Abstract] [Full Text] [PDF]
|
|