In silico segmentations of lentivirus envelope sequences.

ABSTRACT:

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 dif

SUBMITTER: Boissin-Quillon A 

PROVIDER: S-EPMC1847453 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature