2.5 Genome characterization and sequence analysis of the PiCV
genome and cap and rep genes of PiCV strains
The cap gene sequences (n=23), rep gene sequence (n=1) and
the full genome sequences (n=67) of PiCV obtained in this study have
been deposited in GenBank, respectively. The sequences obtained in the
current study were compared with all available PiCV sequence data from
different geographical locations within China (n=54) and the rest of the
world (n=72) from the NCBI nucleotide database as reference sequences.
Multiple sequence alignments were carried out using ClustalW within the
MEGA 5.0 software (Tamura et al., 2011) and the homology among
nucleotide and amino acid sequences was determined by using BioEdit v.
7.0.5 software
(Hall,
1999). A divergence analysis of the cap protein (n=90) of PiCV
was performed using WebLogoTm(http://weblogo.threeplusone.com/), an online software for sequence logo
generator (Crooks et al., 2004). A comparison of entropy (Hx) in amino
acid sequences of cap proteins (n=90) of PiCV was carried out by
using GraphPad Prism 7.00 (GraphPad Software, Inc., USA).