In silico segmentations of lentivirus envelope sequences - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Accéder directement au contenu
Article Dans Une Revue BMC Bioinformatics Année : 2007

In silico segmentations of lentivirus envelope sequences

Résumé

Background: The gene encoding the envelope of lentiviruses exhibits a considerable plasticity, particularly the region which encodes the surface (SU) glycoprotein. Interestingly, mutations do not appear uniformly along the sequence of SU, but they are clustered in restricted areas, called variable ( V) regions, which are interspersed with relatively more stable regions, called constant (C) regions. We look for specific signatures of C/V regions, using hidden Markov models constructed with SU sequences of the equine, human, small ruminant and simian lentiviruses. Results: Our models yield clear and accurate delimitations of the C/V regions, when the test set and the training set were made up of sequences of the same lentivirus, but also when they were made up of sequences of different lentiviruses. Interestingly, the models predicted the different regions of lentiviruses such as the bovine and feline lentiviruses, not used in the training set. Models based on composite training sets produce accurate segmentations of sequences of all these lentiviruses. Conclusion: Our results suggest that each C/V region has a specific statistical oligonucleotide composition, and that the C (respectively V) regions of one of these lentiviruses are statistically more similar to the C (respectively V) regions of the other lentiviruses, than to the V (respectively C) regions of the same lentivirus.
Fichier principal
Vignette du fichier
146815_20110906115801807_1.pdf (475.3 Ko) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

hal-02660412 , version 1 (30-05-2020)

Identifiants

Citer

Aurelia Boissin-Quillon, Didier Piau, Caroline Leroux. In silico segmentations of lentivirus envelope sequences. BMC Bioinformatics, 2007, 8 (99), pp.1-13. ⟨10.1186/1471-2105-8-99⟩. ⟨hal-02660412⟩
21 Consultations
33 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More