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Prédiction markovienne in silico des régions constantes et variables des lentivirus

Abstract : Lentiviruses exhibit a considerable plasticity of the env gene, particularly in the region which encodes the surface (SU) glycoprotein. Interestingly, the SU mutations are clustered in restricted areas, called variable (V) regions and interspaced by more stable regions, called constant regions (C). To determine if the C and V regions are characterized by specific signatures, we developed HMM (Hidden Markov Models), based on the statistical oligonuclotide composition of each type of region, aimed at differentiating the C and V regions of the lentiviruses. We trained hidden Markov models on SU sequences of the equine, human, simian and small ruminant lentiviruses. We obtained a clear delimitation of the C and V regions of all these lentiviruses and of bovine and feline lentiviruses which were not used to define the models. Our results suggest that the C and V regions of the lentiviruses have statistical differences in their composition in words of nucleotides or amino-acids. Specific signatures of the C and V regions have been extracted from our models.
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Contributor : Aurélia Quillon <>
Submitted on : Friday, January 12, 2007 - 2:14:13 PM
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  • HAL Id : tel-00124142, version 1
  • PRODINRA : 252032



Aurélia Quillon. Prédiction markovienne in silico des régions constantes et variables des lentivirus. Mathématiques [math]. Université Claude Bernard - Lyon I, 2006. Français. ⟨tel-00124142⟩



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