ArticleNucleic acids research2012
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
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- HBV genotype distribution and S gene mutations in HIV-HBV co-infected patients: insights from North India.Frontiers in cellular and infection microbiology · 2025Article
- Identification of new circulating recombinant form of HIV-1 CRF139_02B in Japan, and search for the origin.Global health & medicine · 2024Article
- Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor.Genome biology and evolution · 2024Article
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- Genetic diversity in the partial sequence of the HIV-1 gag gene among people living with multidrug-resistant HIV-1 infection.Revista do Instituto de Medicina Tropical de Sao Paulo · 2024Article
- Recombinant Forms of HIV-1 in the Last Decade of the Epidemic in the Russian Federation.Viruses · 2023Article
- Concealed for a Long Time on the Marches of Empires: Hepatitis B Virus Genotype I.Microorganisms · 2023Review
- Genomic Detection of the Emerging, Highly Pathogenic HIV-1 Subtype D in Bahia, Northeast Brazil.Viruses · 2023Article
- The Hepatitis B Virus Genotypes E to J: The Overlooked Genotypes.Microorganisms · 2023Review
- Hepatitis B Virus Genotype E/A Recombinants from Blood Donors in Beira, Mozambique.Microbiology resource announcements · 2023Article
- Hepatitis B virus genotypes and drug resistance mutations circulating in blood donors in Beira, Mozambique.PloS one · 2023Article
- Article
- First report of computational protein-ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients.Biochemistry and biophysics reports · 2022Article
- Identification of hepatitis B virus genotypes detected in Lahaul & Spiti district of Himachal Pradesh, India.The Indian journal of medical research · 2022Article
- Article
- In silico analysis of mutations associated with occult hepatitis B virus (HBV) infection in South Africa.Archives of virology · 2021Article
- Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity afterMicrobial genomics · 2021Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
jpHMM is a very accurate and widely used tool for recombination detection in genomic sequences of HIV-1. Here, we present an extension of jpHMM to analyze recombinations in viruses with circular genomes such as the hepatitis B virus (HBV). Sequence analysis of circular genomes is usually performed on linearized sequences using linear models. Since linear models are unable to model dependencies between nucleotides at the 5'- and 3'-end of a sequence, this can result in inaccurate predictions of recombination breakpoints and thus in incorrect classification of viruses with circular genomes. The proposed circular jpHMM takes into account the circularity of the genome and is not biased against recombination breakpoints close to the 5'- or 3'-end of the linearized version of the circular genome. It can be applied automatically to any query sequence without assuming a specific origin for the sequence coordinates. We apply the method to genomic sequences of HBV and visualize its output in a circular form. jpHMM is available online at http://jphmm.gobics.de for download and as a web server for HIV-1 and HBV sequences.
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