title: A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.
abstract: BACKGROUND
  Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events.
  
  
  RESULTS
  We developed a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach. Given a partition of the aligned input sequence family into known sequence subtypes, our model can jump between states corresponding to these different subtypes, depending on which subtype is locally most similar to a database sequence. Jumps between different subtypes are indicative of intersubtype recombinations. We applied our method to a large set of genome sequences from human immunodeficiency virus (HIV) and hepatitis C virus (HCV) as well as to simulated recombined genome sequences.
  
  
  CONCLUSIONS
  Our results demonstrate that jumps in our jumping profile HMM often correspond to recombination breakpoints; our approach can therefore be used to detect recombinations in genomic sequences. The recombination breakpoints identified by jpHMM were found to be significantly more accurate than breakpoints defined by traditional methods based on comparing single representative sequences.
authors.affiliation: Institute of Microbiology and Genetics, University of Göttingen, Goldschmidtstr, 1, 37077 Göttingen, Germany. aschult2@gwdg.de
authors.forename: Anne-Kathrin
authors.initials: AK
authors.lastname: Schultz
authors.forename: Ming
authors.initials: M
authors.lastname: Zhang
authors.forename: Thomas
authors.initials: T
authors.lastname: Leitner
authors.forename: Carla
authors.initials: C
authors.lastname: Kuiken
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
authors.forename: Burkhard
authors.initials: B
authors.lastname: Morgenstern
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D016679:Genome, Viral; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D016174:Hepacivirus / Q000145:classification / Q000235:genetics*; D008390:Markov Chains; D008957:Models, Genetic; D011995:Recombination, Genetic; D016415:Sequence Alignment