Limits...
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.

Show MeSH

Related in: MedlinePlus

The highly annotated reference sequence (AM282986) in Genbank format visualized by VectorNTI.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2235840&req=5

Figure 2: The highly annotated reference sequence (AM282986) in Genbank format visualized by VectorNTI.

Mentions: As part of our experimental research, a complete HBV genome adw, genotype A, derived from a Taiwanese HBV-infected patient was sequenced (a gift from M-H Lin, National Taiwan University). This HBV clone was known to produce viable HBV particles when transfected into cells [27]. This sequence was highly annotated and submitted to INSDC via EMBL (EMBL ACC: AM282986; Figure 2). The annotation was done by extracting biological information from the literature or other sequence records, based on the functional conservation. This sequence has the most complex annotation per nucleotide (3–13 annotations per base) of any sequence in the public sequence database. It represents the limits of this type of annotation and of parsers implemented to interpret it. It was intended to annotate most experimentally proven features on the sequence. This will lead to annotation of features that may be of lesser importance (e.g. the S protein myristoylation site [28]) or alternative splicing [29,30].


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 highly annotated reference sequence (AM282986) in Genbank format visualized by VectorNTI.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The highly annotated reference sequence (AM282986) in Genbank format visualized by VectorNTI.
Mentions: As part of our experimental research, a complete HBV genome adw, genotype A, derived from a Taiwanese HBV-infected patient was sequenced (a gift from M-H Lin, National Taiwan University). This HBV clone was known to produce viable HBV particles when transfected into cells [27]. This sequence was highly annotated and submitted to INSDC via EMBL (EMBL ACC: AM282986; Figure 2). The annotation was done by extracting biological information from the literature or other sequence records, based on the functional conservation. This sequence has the most complex annotation per nucleotide (3–13 annotations per base) of any sequence in the public sequence database. It represents the limits of this type of annotation and of parsers implemented to interpret it. It was intended to annotate most experimentally proven features on the sequence. This will lead to annotation of features that may be of lesser importance (e.g. the S protein myristoylation site [28]) or alternative splicing [29,30].

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