Sentence examples for acid sequences were done using the from inspiring English sources

Sequence assembly and multiple alignment of nucleotide and amino acid sequences were done using the DNAMAN software package (Lynnon Biosoft, Canada).

Multiple sequence alignment of the amino acid sequences was done using the program ClustalW [ 47].

Alignment of amino acid sequences was done using the ClustalW2 program http://www.ebi.ac.uk/Tools/clustalw2/.ac.uk/Tools/clustalw2/

A homology search for putative amino acid sequences was done using BLASTP on the National Center for Biotechnology Information (NCBI) website (http://www.ncbi.nlm.nih.gov/).nih.gov/

6 Multiple alignment of coding DNA from aligned amino acid sequences was done using RevTrans.

Analysis of sequences was done using BiQ Analyzer.

Multiple sequence alignment of the E2 sequences and the reference HPV16 sequence (HPV16 R) from the HPV16 Sequence Database (Los Alamos National Laboratory) was done using the multiple sequence alignment program Bio Edit in order to detect nucleic acid variations.

Sequencing was done using Illumina sequencing platforms.

Initially, BLASTP [130] searches against the NCBI protein database were done using R. felis amino acid sequences as queries (for BLASTP specifics and threshold see below).

Amino acid sequences were aligned using CLUSTALW (v 1.82) with default parameters [ 15] and the subsequent phylogenetic analyses were done using PHYLIP with default parameters [ 16].

Visualisation, calculation of a background frequency corrected sequence logo, and calculation of amino acid conservation was done using LaTeX and TEXshade [ 100].