Figure 1

Regions predicted by the hidden Markov models on the nucleotide sequence of EIAV SU. The graphic displays the regions predicted by our mathematical model (—). The schematic organization of EIAV SU, with the position of the 8 variable regions V1 to V8 (hatched boxes) and of the 9 constant regions (—), as defined by classical amino-acid multiple alignments, is represented under the graphic. (A) HMM of order 5 with 2 hidden states, trained on the variable (V) and constant (C) regions. (B) HMM of order 5 with 9 hidden states, trained on the 8 V regions and on the reunion of the C regions.