ArticleSpringerPlus2016
Bioinformatic curation and alignment of genotyped hepatitis B virus (HBV) sequence data from the GenBank public database.
Article in SpringerPlus, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A systematic review of hepatitis B virus (HBV) drug and vaccine escape mutations in Africa: A call for urgent action.PLoS neglected tropical diseases · 2018Pooled it
- Applications of next-generation sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations.Journal of biomedical science · 2018Pooled it
- The Molecular Epidemiology of Hepatitis B Virus and Its Resistance-Associated Mutations in the Polymerase Gene in the Americas.Microorganisms · 2025Article
- Hepatitis B virus (HBV) viremia despite tenofovir disoproxil fumarate-containing antiretroviral therapy in persons with HBV/HIV coinfection.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2024Article
- Hepatitis B Virus Genotype E/A Recombinants from Blood Donors in Beira, Mozambique.Microbiology resource announcements · 2023Article
- The Complex Role of HBeAg and Its Precursors in the Pathway to Hepatocellular Carcinoma.Viruses · 2023Review
- HexSE: Simulating evolution in overlapping reading frames.Virus evolution · 2023Article
- Integrated hepatitis B virus DNA maintains surface antigen production during antiviral treatment.The Journal of clinical investigation · 2022Article
- In silico analysis of mutations associated with occult hepatitis B virus (HBV) infection in South Africa.Archives of virology · 2021Article
- Review
- In Silico Prediction of Human Leukocytes Antigen (HLA) Class II Binding Hepatitis B Virus (HBV) Peptides in Botswana.Viruses · 2020Article
- Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences.The Journal of general virology · 2020Article
- Global and regional dispersal patterns of hepatitis B virus genotype E from and in Africa: A full-genome molecular analysis.PloS one · 2020Article
- Identification of hepatitis B virus genotype A/E recombinants in Ghana.Virus genes · 2019Article
- Identification of hepatitis B virus genotype I in Thailand.Journal of medical virology · 2019Article
- A novel hepatitis B virus recombinant genotype D4/E identified in a South African population.Heliyon · 2019Article
- CCT: a coordinate conversion tool for hepatitis B virus.Southern African journal of infectious diseases · 2019Article
- Article
- In Silico Analysis of Hepatitis B Virus Occult Associated Mutations in Botswana Using a Novel Algorithm.Genes · 2018Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHepatitis B virus (HBV) DNA sequence data from thousands of samples are present in the public sequence databases. No publicly available, up-to-date, multiple sequence alignments, containing full-length and subgenomic fragments per genotype, are available. Such alignments are useful in many analysis applications, including data-mining and phylogenetic analyses.
resultsBy issuing a query, all HBV sequence data from the GenBank public database was downloaded (67,893 sequences). Full-length and subgenomic sequences, which were genotyped by the submitters (30,852 sequences), were placed into a multiple sequence alignment, for each genotype (genotype A: 5868 sequences, B: 4630, C: 7820, D: 8300, E: 2043, F: 985, G: 189, H: 108, I: 23), according to the results of offline BLAST searches against a custom reference library of full-length sequences. Further curation was performed to improve the alignment.
conclusionsThe algorithm described in this paper generates, for each of the nine HBV genotypes, multiple sequence alignments, which contain full-length and subgenomic fragments. The alignments can be updated as new sequences become available in the online public sequence databases. The alignments are available at http://hvdr.bioinf.wits.ac.za/alignments.
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Registered trials
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