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Protocols

HBVdb specifications

Information


Unique identifier OMICS_03069
Name HBVdb
Alternative name Hepatitis B Virus database
Restrictions to use None
Maintained No

Taxon


  • Viruses
    • Hepatitis B virus

Publication for Hepatitis B Virus database

HBVdb citations

 (5)
library_books

Single Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma

2016
J Virol
PMCID: 5110153
PMID: 27681123
DOI: 10.1128/JVI.01625-16

[…] with AAV-HBV, using BWA v0.5.9 () with default parameters on the MOIRAI pipeline (). The unmapped tags extracted from the mapping results were aligned to 16 representative HBV genomes downloaded from HBVdb (). Because the HBV genome is circular, each genome was tandemly repeated for mapping all genome sequences. After alignment of tag sequences with 16 representative HBV genomes, the HBV genotype […]

call_split

Lamivudine/Adefovir Treatment Increases the Rate of Spontaneous Mutation of Hepatitis B Virus in Patients

2016
PLoS One
PMCID: 5029863
PMID: 27649318
DOI: 10.1371/journal.pone.0163363
call_split See protocol

[…] 6 (www.megasoftware.net) to assess whether patients corresponded to monophyletic sequence groups, and the HBV genotype was determined using the genotyping tool available from the French HBV database (hbvdb.ibcp.fr). Sequences were visualized with MEGA6 and Jalview (www.jalview.org) and phylogenetic trees were edited with TreeDyn (www.treedyn.org). […]

library_books

Molecular Characterization of Pre Core/Core and S Region of Hepatitis B Virus in Hemodialysis Patients With Occult Hepatitis B Infection

2015
PMCID: 4644307
PMID: 26587212
DOI: 10.5812/jjm.23686

[…] both nested PCR products and TA cloning products of S and pre-core/core regions was performed by Bioneer (Korea). The results were analyzed by MEGA 5.2, Gene Runner, and web-based tools such as NCBI, Hepatitis B Virus Database, and Geno2pheno. The reference sequence from GeneBank with accession number NC-003977.1 was used to compare and detect the presence of mutations in isolated HBV samples from […]

call_split

Detection of hepatitis B virus isolates with mutations associated with immune escape mutants among pregnant women in Ibadan, southwestern Nigeria

2015
Springerplus
PMCID: 4320141
PMID: 25674500
DOI: 10.1186/s40064-015-0813-1
call_split See protocol

[…] es at positions 122, 127, 134 and 160 were initially used to determine HBV genotypes and serotypes (Forbi et al.). Subsequently, HBsAg reference sequences were retrieved from the HBV database (http://hbvdb.ibcp.fr/HBVdb/) and aligned using the CLUSTAL W program in MEGA 5 software with default settings (Tamura et al.). Afterwards, a neighbor-joining tree was constructed using MEGA 5 software with t […]

library_books

Whole exome sequencing reveals mutations in NARS2 and PARS2, encoding the mitochondrial asparaginyl tRNA synthetase and prolyl tRNA synthetase, in patients with Alpers syndrome

2014
PMCID: 4299715
PMID: 25629079
DOI: 10.1002/mgg3.115

[…] .836C>T, p.S279L) is a missense mutation, predicted by SIFT to be damaging (although it is predicted to be benign by PolyPhen-2) and is not listed as dbSNP (build 135) nor in any of the NHLBI ESP nor HBVDB databases. S279 is located in a 34 amino acid long cluster between motifs 2 and 3 which does not belong to the class II aaRS-like core domain. A BLAST search to identify homologous clusters in o […]

Citations

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HBVdb institution(s)
Unité Bases Moléculaires et Structurales des Systèmes Infectieux, Lyon, France

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