Figure 3

CODEHOP PCR primers derived from the VYGF/TGV sequence motif. (A) Multiple sequence alignment of 11 herpesvirus DNA polymerase sequences contained within the conserved VYGF/TGV domain as an output of BlockMaker [32]. (B) Sequences from 6 additional herpesvirus species aligned with the conserved sequence block. (C) The consensus amino acid sequence from the VYGF/TGV motif as determined by the CODEHOP algorithm is presented (in bold and boxed) and the other amino acids found at each position are aligned vertically above the consensus amino acid. The sense-strand "VYG1A" CODEHOP predicted by the CODEHOP software is indicated with the 5' consensus clamp in uppercase and the 3' degenerate core region in lowercase. The sequence, relative position and encoded sequences of the manually designed CODEHOPs, "TGV" and "VYGA" are also shown (see Table 1). Highlighted amino acids are discussed in the text. The degeneracy of the primer pools is indicated in parentheses. DNA polymerase protein sequences were derived from the following herpesvirus species: HSV1, NC_001806; VZV, NC_001348; HHV6, NC_001664; CMV, AF033184; HHV7, NC_001716; RhCMV, AF033184; hCMV, AF033184;; HSV2, NC_001798; RFHVMm, AF005479; MHV68, NC_001826; KSHV, AF005477; HVS, NC_001350; AtHV3, NC_001987; AlHV1, NC_002531; RRV, AF029302; IHV, NC_001493; EBV, NC_001345; EHV2, NC_001650.