A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

2006 | journal article. A publication with affiliation to the University of Göttingen.

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​A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes​
Schultz, A.-K.; Zhang, M.; Leitner, T.; Kuiken, C.; Korber, B.; Morgenstern, B.   & Stanke, M.​ (2006) 
BMC Bioinformatics7 art. 265​.​ DOI: https://doi.org/10.1186/1471-2105-7-265 

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Authors
Schultz, Anne-Kathrin; Zhang, M.; Leitner, Thomas; Kuiken, Carla; Korber, Bette; Morgenstern, Burkhard ; Stanke, Mario
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. Conclusion: 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.
Issue Date
2006
Status
published
Publisher
Biomed Central Ltd
Journal
BMC Bioinformatics 
ISSN
1471-2105
Sponsor
NIAID NIH HHS [Y01 AI1500, Y1-AI-1500-01]

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