Identification and Characterization of Pathogenicity and Other Genomic Islands Using Base Composition Analyses

• Hacker J , Blum-OehlerG, MühldorferI, TschäpeH: Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution.Mol. Microbiol.23 , 1089–1097 (1997).
   PubMed Web of Science ®Google Scholar
• Schmidt H , HenselM: Pathogenicity islands in bacterial pathogenesis.Clin. Microbiol. Rev.17 , 14–56 (2004).
   PubMed Web of Science ®Google Scholar
• Hacker J , KaperJB: Pathogeniciy islands and the evolution of microbes.Annu. Rev. Microbiol.54 , 641–679 (2000).
   PubMed Web of Science ®Google Scholar
• Hacker J , CarnielE: Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes.EMBO Rep.2 , 376–381 (2001).
   PubMed Web of Science ®Google Scholar
• Koonin EV , MakarovaKS, AravindL: Horizontal gene transfer in prokaryotes: quantification and classification.Annu. Rev. Microbiol.55 , 709–742 (2001).
   PubMed Web of Science ®Google Scholar
• Ochman H , LawrenceJG, GroismanEA: Lateral gene transfer and the nature of bacterial innovation.Nature405 , 299–304 (2000).
   PubMed Web of Science ®Google Scholar
• Gill SR , FoutsDE, ArcherGL et al.: Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J. Bacteriol.187 , 2426–2438 (2005).
   PubMed Web of Science ®Google Scholar
• Sueoka N , MarmurJ, DotyP 2nd: Dependence of the density of deoxyribonucleic acids on guanine-cytosine content. Nature183 , 1429–1431 (1959).
   PubMed Web of Science ®Google Scholar
• Grantham R , GautierC, GouyM, MercierR, PaveA: Codon catalog usage and the genome hypothesis.Nucleic Acids Res.8 , R49–R62 (1980).
   PubMed Web of Science ®Google Scholar
• Médigue C , RouxelT, VigierP, HenautA, DanchinA: Evidence for horizontal gene transfer in Escherichia coli speciation.J. Mol. Biol.222 , 851–856 (1991).
   PubMed Web of Science ®Google Scholar
• Abe T , KanayaS, KinouchiM, IchibaY, KozukiT, IkemuraT: Informatics for unveiling hidden genome signatures.Genome Res.13 , 693–702 (2003).
   PubMed Web of Science ®Google Scholar
• Sandberg R , WinbergG, Branden C-I, Kaske A, Ernberg I, Coster J: Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res.11 , 1404–1409 (2001).
   PubMed Web of Science ®Google Scholar
• Karlin S : Global dinucleotide signatures and analysis of genomic heterogeneity.Curr. Opin. Microbiol.1 , 598–610 (1998).
   PubMed Web of Science ®Google Scholar
• Lawrence JG , OchmanH: Amelioration of bacterial genomes: rates of change and exchange.J. Mol. Evol.44 , 383–397 (1997).
   PubMed Web of Science ®Google Scholar
• Ragan MA , HarlowTJ, BeikoRG: Do different surrogate methods detect lateral genetic transfer events of different relative ages?Trends Microbiol.14 , 4–8 (2006).
   PubMed Web of Science ®Google Scholar
• Higgs PG , AttwoodTK: Bioinformatics and Molecular Evolution. Blackwell, MA, USA (2005).
   Google Scholar
• Lio P , VannucciM: Finding pathogenicity islands and gene transfer events in genome data.Bioinformatics16 , 932–940 (2000).
   PubMed Web of Science ®Google Scholar
• Zhang R , ZhangCT: A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I.Bioinformatics20 , 612–627 (2004).
   PubMed Web of Science ®Google Scholar
• Zhang CT , ZhangR, OuHY: The Z curve database: a graphic representation of genome sequences.Bioinformatics19 , 593–599 (2003).
   PubMed Web of Science ®Google Scholar
• Chen L -L: Identification of genomic islands in six plant pathogens. Gene374 , 134–141 (2006).
   PubMed Web of Science ®Google Scholar
• Mrazek J , KarlinS: Detecting alien genes in bacterial genomes.Ann. NY Acad. Sci.870 , 314–329 (1999).
   PubMed Web of Science ®Google Scholar
• Merkl R : SIGI: score-based identification of genomic islands.BMC Bioinformatics5 , 22 (2004).
   PubMed Web of Science ®Google Scholar
• Waack S , KellerO, AsperR et al.: Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics7 , 142 (2006).
   PubMed Web of Science ®Google Scholar
• Rutherford K , ParkhillJ, CrookJ et al.: Artemis: sequence visualization and annotation. Bioinformatics16 , 944–945 (2000).
   PubMed Web of Science ®Google Scholar
• Karlin S : Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes.Trends Genet.9 , 335–343 (2001).
   Google Scholar
• van Passel MWJ , LuyfACM, van Kampen AHC, Bart A, van der Ende A: δρ-Web, an online tool to assess composition similarity of individual nucleic acid sequences. Bioinformatics21 , 3053–3055 (2005).
   PubMed Web of Science ®Google Scholar
• Hooper SD , BergOG: Detection of genes with atypical nucleotide sequence in microbial genomes.J. Mol. Evol.54 , 365–375 (2002).
   PubMed Web of Science ®Google Scholar
• Nakamura Y , ItohT, MatsudaH, Gojobori T: Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet.36 , 760–766 (2004).
   PubMed Web of Science ®Google Scholar
• Vernikos GS , ParkhillJ: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.Bioinformatics22(18) , 2196–2203 (2006).
   PubMed Web of Science ®Google Scholar
• Dufraigne C , FertilB, LespinatsS, GironA, DeschavanneP: Detection and characterization of horizontal transfers in prokaryotes using genomic signature.Nucleic Acids Res.33 , E6 (2005).
   PubMed Web of Science ®Google Scholar
• Lawrence JG , OchmanH: Molecular archaeology of the Escherichia coli genome.Proc. Natl Acad. Sci. USA95 , 9413–9417 (1998).
   PubMed Web of Science ®Google Scholar
• Garcia-Vallvé S , GuzmanE, MonteroMA, RomeuA: HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes.Nucleic Acids Res.31 , 187–189 (2003).
   PubMed Web of Science ®Google Scholar
• Garcia-Vallvé S , RomeuA, PalauJ: Horizontal gene transfer in bacterial and archaeal complete genomes.Genome Res.10 , 1719–1725 (2000).
   PubMed Web of Science ®Google Scholar
• Tu Q , DingD: Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis.FEMS Microbiol. Lett.221 , 269–275 (2003).
   PubMed Web of Science ®Google Scholar
• Hsiao W , WanI, JonesSJ, BrinkmanFSL: IslandPath: aiding detection of genomic islands in prokaryotes.Bioinformatics19 , 418–420 (2003).
   PubMed Web of Science ®Google Scholar
• Hsiao WWL , UngK, AeschlimanD, Bryan J, Finlay BB, Brinkman FSL: Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet.1 , E62 (2005).
   PubMedGoogle Scholar
• Mantri Y , WilliamsKP: Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities.Nucleic Acids Res.32 , D55–D58 (2004).
   PubMed Web of Science ®Google Scholar
• Ou H -Y, Chen L-L, Lonnen J et al.: 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.34 , E3 (2006).
   PubMedGoogle Scholar
• Canchaya C , FournousG, BrussowH: The impact of prophages on bacterial chromosomes.Mol. Microbiol.53 , 9–18 (2004).
   PubMed Web of Science ®Google Scholar
• Greub G , CollynF, GuyL, Roten C-A: A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system. BMC Microbiol.4 , 48 (2004).
   PubMed Web of Science ®Google Scholar
• Stothard P : The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences.Biotechniques28 , 1102–1104 (2000).
   PubMed Web of Science ®Google Scholar
• van P assel MWJ, Bart A, Waaijer RJA, Luyf ACM, van Kampen AHC, van der Ende A: An in vitro strategy for the selective isolation of anomalous DNA from prokaryotic genomes. Nucleic Acids Res.32 , E114 (2004).
   PubMedGoogle Scholar
• Azad RK , LawrenceJG: Use of artificial genomes in assessing methods for atypical gene detection.PloS Comput. Biol.1 , E56 (2005).
   PubMed Web of Science ®Google Scholar
• Ragan MA : On surrogate methods for detecting lateral gene transfer.FEMS Microbiol. Lett.201 , 187–191 (2001).
   PubMed Web of Science ®Google Scholar
• Collyn F , GuyL, MarceauM, SimonetM, RotenCAH: Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics.Bioinformatics22 , 1072–1079 (2006).
   PubMed Web of Science ®Google Scholar
• van Passel MWJ , BartA, ThygesenHH, LuyfACM, van Kampen AHC, van der Ende A: An acquisition account of genomic islands based on genome signature comparisons. BMC Genomics6 , 163 (2005).
   PubMedGoogle Scholar
• Service RF : Gene sequencing: the race for the $1000 genome.Science311 , 1544–1546 (2006).
   PubMed Web of Science ®Google Scholar

Websites

• ENTREZ Genome Project www.ncbi.nlm.nih.gov/genomes/lproks.cgi
   Google Scholar
• Genomes online database v 2.0 www.genomesonline.org
   Google Scholar
• Sequence Manipulation Suite http://bioinformatics.org/sms2
   Google Scholar
• NCBI: GenBank overview www.ncbi.nih.gov/Genbank
   Google Scholar
• Wikipedia www.en.wikipedia.org/wiki/Transistor_count
   Google Scholar
• Z Curve Database of Genomes http://tubic.tju.edu.cn/zcurve
   Google Scholar
• Theoretical computer science www.tcs.informatik.uni-goettingen.de/colombo
   Google Scholar
• δρweb and compare_islands http://deltarho.amc.nl/
   Google Scholar
• Wellcome Trust Sanger Institute www.sanger.ac.uk/Software/analysis/alien_ hunter
   Google Scholar
• Horizontal gene transfer database www.tinet.org/~debb/HGT/
   Google Scholar
• Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis http://compbio.sibsnet.org/projects/pai-ida
   Google Scholar
• IslandPath www.pathogenomics.sfu.ca/islandpath
   Google Scholar
• Islander: database of genomic islands http://129.79.232.60/cgi-bin/islander/islander.cgi
   Google Scholar