| Title |
Bioinformatic curation and alignment of genotyped hepatitis B virus (HBV) sequence data from the GenBank public database
|
|---|---|
| Published in |
SpringerPlus, October 2016
|
| DOI | 10.1186/s40064-016-3312-0 |
| Pubmed ID | |
| Authors |
Trevor G. Bell, Mukhlid Yousif, Anna Kramvis |
| Abstract |
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. By 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. 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. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 63 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 1 | 2% |
| Unknown | 62 | 98% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Master | 20 | 32% |
| Researcher | 11 | 17% |
| Student > Ph. D. Student | 5 | 8% |
| Student > Doctoral Student | 4 | 6% |
| Student > Bachelor | 4 | 6% |
| Other | 9 | 14% |
| Unknown | 10 | 16% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 21 | 33% |
| Agricultural and Biological Sciences | 13 | 21% |
| Immunology and Microbiology | 8 | 13% |
| Computer Science | 3 | 5% |
| Engineering | 2 | 3% |
| Other | 5 | 8% |
| Unknown | 11 | 17% |
Attention Score in Context
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#20,349,664
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