Related Experiment Video
Updated: Jul 16, 2026
07:28
Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
Published on: January 10, 2025
In silico segmentations of lentivirus envelope sequences
Aurélia Boissin-Quillon1, Didier Piau, Caroline Leroux
1UMR754 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>
BMC Bioinformatics
|March 23, 2007
Summary
Hidden Markov models accurately identify constant/variable regions in lentivirus surface glycoproteins. These models reveal conserved sequence patterns across different lentivirus species, aiding in understanding viral evolution.
Area of Science:
- Virology
- Molecular Biology
- Bioinformatics
Background:
- Lentivirus envelope genes, particularly the surface (SU) glycoprotein, show high plasticity.
- Mutations in SU are clustered in variable (V) regions, interspersed with stable constant (C) regions.
Purpose of the Study:
- To identify specific signatures of C/V regions in lentiviruses.
- To develop models for accurate delimitation of C/V regions.
Main Methods:
- Utilized hidden Markov models (HMMs).
- Trained HMMs on SU sequences from equine, human, small ruminant, and simian lentiviruses.
- Tested model accuracy on both same-species and cross-species lentivirus sequences.
Main Results:
- HMMs accurately delineated C/V regions across various lentivirus species, including those not used in training (bovine, feline).
- Models trained on composite datasets demonstrated robust segmentation capabilities for all tested lentiviruses.
- Each C/V region exhibits a distinct statistical oligonucleotide composition.
Conclusions:
- C/V regions possess unique sequence signatures.
- C regions are statistically more similar to C regions of other lentiviruses, and V regions to other V regions, than to the opposite region within the same lentivirus.
- This suggests conserved evolutionary pressures shaping these regions across different lentiviruses.
