In silico segmentations of lentivirus envelope sequences.
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.


CONCLUSIONS
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.
Boissin-Quillon
Aurélia
A
UMR754 INRA-ENVL-UCBL Rétrovirus et Pathologie Comparée, IFR 128 BioSciences Lyon-Gerland, Université Claude Bernard Lyon 1, Lyon, France. aurelia.quillon@univ-lyon1.fr <aurelia.quillon@univ-lyon1.fr>
Piau
Didier
D
Leroux
Caroline
C
D000465:Algorithms; D000818:Animals; D017124:Conserved Sequence / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D006801:Humans; D016086:Lentivirus / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014759:Viral Envelope Proteins / Q000235:genetics*
D014759:Viral Envelope Proteins