Figure 2

Regions predicted by the hidden Markov models on the deduced amino-acid 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) First order HMM with 2 hidden states, trained on the V and C regions. (B) First order HMM with 9 hidden states, trained on the 8 V regions and on the reunion of the C regions. (C) First order HMM with 9 hidden states tested on an artificial sequence, where 15 amino-acids of the V7 sequence are inserted into the constant region C2 located between V1 and V2.