title: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
abstract: BACKGROUND
  There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes.
  
  
  RESULTS
  We introduce a novel computational method, Interpolated Variable Order Motifs (IVOMs), which exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared with fixed-order methods. For optimal localization of the boundaries of each predicted region, a second order, two-state hidden Markov model (HMM) is implemented in a change-point detection framework. We applied the IVOM approach to the genome of Salmonella enterica serovar Typhi CT18, a well-studied prokaryote in terms of HGT events, and we show that the IVOMs outperform state-of-the-art low and high order motif methods predicting not only the already characterized Salmonella Pathogenicity Islands (SPI-1 to SPI-10) but also three novel SPIs (SPI-15, SPI-16, SPI-17) and other HGT events.
  
  
  BACKGROUND
  The software is available under a GPL license as a standalone application at http://www.sanger.ac.uk/Software/analysis/alien_hunter
  
  
  BACKGROUND
  gsv@sanger.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK. gsv@sanger.ac.uk
authors.forename: Georgios S
authors.initials: GS
authors.lastname: Vernikos
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D004269:DNA, Bacterial / Q000235:genetics*; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics; D044404:Genomic Islands / Q000235:genetics*; D012475:Salmonella / Q000235:genetics* / Q000472:pathogenicity*; D014774:Virulence / Q000235:genetics*; D037521:Virulence Factors / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D037521:Virulence Factors