An integrated linux environment for HBV evolutionary analysis based on GDE for Linux:
 
 
Developed by:  Dimitris  and Tulio de Oliveira, at Rega Institute, Belgium.
version 1.0, 16/03/2002, updated Sept. 2004

GDE for Linux menu download:


Contents: HBV Sequence datasets, HBV Sequence databases, Bioinformatics software, References and Online resources

HBV Sequence datasets 

1. Reference sequence : 
HPBADRA Hepatitis B virus, complete genome,  DNA, 3215 bp 
FASTA file, GenBank file, Ref Seq. NCBI, Genome picture.

Genome picture:
Figure of the HBV genome

2. Genetic variants dataset: 
FASTA file , details (24 complete genome strains)

3. Dataset for phylogenetic analysis:
complete genome - FASTA file , details (24 complete genome strains).
 

Sequence Databases for local blast and Xylem access:

1. Genbank database (strains, date, where, size)
HBV Sequence download at HBV Sequence Db (Japan)
 

Bioinformatics Software:
A large number of software had been integrated, list of the software
The software need to be installed in your system following the instructions. [PDF file]

Online Resources:

Sequence  Databases:
Hepatitis B Virus Database at DNA database of Japan
Viral Genome resource at NCBI 

Taxonomy:
International Committee on Taxonomy of Viruses
HBV Taxonomy report NCBI 
Phylogenetic Tree at the HBV sequence database (Japan)

Alignments search and repositories:
Hepatitis B Virus Database at DNA database of Japan
 

     
4. Reference  papers for phylogenetic analysis:
A new genotype of hepatitis B virus: complete genome and phylogenetic relatedness.
Stuyver L, De Gendt S, Van Geyt C, Zoulim F, Fried M, Schinazi RF, Rossau R.

 

 


The BioAfrica web site  is maintained by: Dr. Tulio de Oliveira,
Revised 10th of November 2005 - Copyright @ BioAfrica.