Abstract
Background Hepatitis 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.Conclusions The 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.
Highlights
Hepatitis B virus (HBV) DNA sequence data from thousands of samples are present in the public sequence databases
Evolutionary relationships between samples are elucidated by phylogenetic analyses, which typically involve DNA sequences from many organisms of interest, and from many related samples for comparison
The aim of the present study is to provide updated, curated, alignments of each HBV genotype (A to I), consisting of all available full-length and subgenomic fragments from the GenBank public database, where the genotype could be mined from the GenBank submission
Summary
Hepatitis B virus (HBV) DNA sequence data from thousands of samples are present in the public sequence databases. 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. Results: By issuing a query, all HBV sequence data from the GenBank public database was downloaded (67,893 sequences). Conclusions: The algorithm described in this paper generates, for each of the nine HBV genotypes, multiple sequence alignments, which contain full-length and subgenomic fragments. Public sequence databases Direct (Sanger) DNA sequencing (Sanger et al 1977) is a relatively inexpensive and routine procedure in molecular biology. With support from the National Institutes of Health, this database was
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