Figure 9

Similarity Plot of Full-length MuLV genomes: Plots of similarity between the MuLV 1313 genome (the 'query' sequence) and 10 representative, full-length MuLV genomes (the 'reference' sequences) present in the GenBank database were generated by SimPlot [72]. This program plots similarity versus position and calculates percent identity of a query sequence to a panel of reference sequences after their alignment in a sliding window, which is moved across the alignment in steps. The window and step sizes are adjustable. Prior to this analysis, an alignment of the full-length MuLV genomes was generated by the Clustal W program [64, 80]. Each curve is a comparison between the query genome being analyzed and one of the reference genomes after an alignment of the genomes has been made and positions containing gaps within the alignment were removed. Sequences used in the analysis include: AKV MuLV (AKV, J01998), Cas-Br-E MuLV (CAS-BR-E, X57540), Friend-57 MuLV (FR-MuLV 57, X02794), Friend FB29 MuLV (FR-MuLV FB29, Z11128), Friend PVC211 MuLV (FR-MuLV PVC211, M93134), mink cell focus-forming virus 1233 (MCF1233, U13766), Moloney MuLV (Moloney, J02255), Rauscher MuLV (Rauscher, U94692), SL3-3 MuLV (SL3-3, AF169256) and solid-type reticulum cell sarcoma 19-6 MuLV (SRS 19-6, AF019230). All 'reference' sequences used in the analysis with the exception of the polytropic MCF1233 display ecotropic in-vitro host range. Above the curves is a schematic diagram (drawn to scale) showing the relative positions of the coding regions of the gag (MA, pp12, CA and CA), pol (PR, RT and IN) and env (SU and TM) genes of the MuLV genome.