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HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences.

Panjaworayan N, Roessner SK, Firth AE, Brown CM - Virol. J. (2007)

Bottom Line: In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx).Novel regulatory motifs can be found by analysing the annotated sequences.HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand. panna478@student.otago.ac.nz

ABSTRACT

Background: The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (approximately 3.2 kb) but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses.

Results: These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx). It also contains analyses based on curated HBV alignments. Information about conserved regions - including primary conservation (e.g. CDS-Plotcon) and RNA secondary structure predictions (e.g. Alidot) - is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser) adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences.

Conclusion: HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

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Related in: MedlinePlus

The top part of the screenshot showing annotations of the AM282986m Hepatitis B virus genome. Calculated ORFs are represented as bars. This analysis indicates ORFs that could potentially be initiated at different ATG codons. For example, the predicted nested ORF 1 (marked by box).
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Figure 5: The top part of the screenshot showing annotations of the AM282986m Hepatitis B virus genome. Calculated ORFs are represented as bars. This analysis indicates ORFs that could potentially be initiated at different ATG codons. For example, the predicted nested ORF 1 (marked by box).

Mentions: Where annotated, CDSs are shown. For consistency, and for HBV genomes for which not all CDS sequences are annotated, potential ORFs >100 aa were calculated with getorf (EMBOSS). Coding regions, which extended over the virtual end of the viral genome sequence were automatically assigned and represented as two parts (e.g. Figure 5). This process also shows ORFs that could potentially be initiated at different ATG codons. For example (Figure 5) the predicted S ORFs, ORF 2 and 3, for which there is experimental evidence, or the predicted nested ORF 1, which could arise by internal initiation within P.


HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences.

Panjaworayan N, Roessner SK, Firth AE, Brown CM - Virol. J. (2007)

The top part of the screenshot showing annotations of the AM282986m Hepatitis B virus genome. Calculated ORFs are represented as bars. This analysis indicates ORFs that could potentially be initiated at different ATG codons. For example, the predicted nested ORF 1 (marked by box).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2235840&req=5

Figure 5: The top part of the screenshot showing annotations of the AM282986m Hepatitis B virus genome. Calculated ORFs are represented as bars. This analysis indicates ORFs that could potentially be initiated at different ATG codons. For example, the predicted nested ORF 1 (marked by box).
Mentions: Where annotated, CDSs are shown. For consistency, and for HBV genomes for which not all CDS sequences are annotated, potential ORFs >100 aa were calculated with getorf (EMBOSS). Coding regions, which extended over the virtual end of the viral genome sequence were automatically assigned and represented as two parts (e.g. Figure 5). This process also shows ORFs that could potentially be initiated at different ATG codons. For example (Figure 5) the predicted S ORFs, ORF 2 and 3, for which there is experimental evidence, or the predicted nested ORF 1, which could arise by internal initiation within P.

Bottom Line: In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx).Novel regulatory motifs can be found by analysing the annotated sequences.HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand. panna478@student.otago.ac.nz

ABSTRACT

Background: The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (approximately 3.2 kb) but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses.

Results: These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx). It also contains analyses based on curated HBV alignments. Information about conserved regions - including primary conservation (e.g. CDS-Plotcon) and RNA secondary structure predictions (e.g. Alidot) - is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser) adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences.

Conclusion: HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

Show MeSH
Related in: MedlinePlus