The subtyping process consists of three steps: The initiat steps involves the identification of the genomic region at the GK18 HHV8 reference sequence. This process uses BLAST software. The second step involves the alignment of the query sequences with the complete K1 reference sequences for HHV8 subtypes A, A5, B, C, D and E. More information on this alignment is found in a Table 1. The final step involves construction of a phylogenetic tree using HKY distance method with gamma distribution in PAUP* software. The HHV8 subtypes and sub-groups are identified using JAVA software. Table 1: Reference sequences
for HHV8 subtyping:
Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK, HIV-1 Immunopathogenesis and Therapeutics Program at University of Pretoria, South Africa. Funded by the Marie Curie Fellowship, Wellcome Trust and the Royal Society, UK. Suggestions or problems on the program please contact: Dr Tulio de Oliveira. |