A primary study of evolution of hepatitis B virus based on motif discovery.
- Author:
Lei MA
;
Qing-Qing YI
;
Qi ZHANG
;
Jian-Feng HE
- Publication Type:Journal Article
- MeSH:
Computational Biology;
Conserved Sequence;
Evolution, Molecular;
Hepatitis B virus;
genetics;
Humans;
Nucleotide Motifs;
Phylogeny;
Reproducibility of Results
- From:
Chinese Journal of Virology
2014;30(1):13-18
- CountryChina
- Language:Chinese
-
Abstract:
Hepatitis B is a serious infectious disease worldwide, and hepatitis B virus (HBV) is the direct cause of this disease. In recent years, as an essential part of its evolutionary process, HBV mutation has been extensively studied domestically and globally. However, the study on the conserved sequences in HBV sequences is still in its infancy. In this study, we applied multiple EM for motif elicitation (MEME) algorithm to discover HBV motif and proposed a new metric, conservative index (CI), to carry out phylogenetic analysis based on HBV sequences. Then, the constructed phylogenetic tree was subjected to reliability assessment. The results demonstrated that the new metric CI combined with the MEME algorithm can effectively help to discover motifs in HBV sequences and construct a phylogenetic tree based on them and to analyze the evolutionary relationship between HBV sequences; in addition, the possible ancestral sequences of samples may be obtained by conservative analysis. The proposed method is valuable for the exploratory study on large HBV sequence data sets.
