SEQHEPB: A sequence analysis program and relational database system for chronic hepatitis B

• Published in: Antiviral research 2007-07, Vol.75 (1), p.64-74
• Main Authors: Yuen, Lilly K.W., Ayres, Anna, Littlejohn, Margaret, Colledge, Danielle, Edgely, Andrew, Maskill, William J., Locarnini, Stephen A., Bartholomeusz, Angeline
• Format: Article
• Language: English
• Subjects: Antibiotics. Antiinfectious agents. Antiparasitic agents; Antiviral agents; Biological and medical sciences; Data mining; Databases, Genetic; DNA Mutational Analysis; Drug resistance; Drug Resistance, Viral - genetics; Genotype; Hepatitis B virus; Hepatitis B virus - genetics; Hepatitis B, Chronic - genetics; Human viral diseases; Humans; Infectious diseases; Medical sciences; Mutation; Pharmacology. Drug treatments; Reference Standards; Relational database; Sequence Analysis, DNA; Software Design; Viral diseases; Viral hepatitis
• ISSN: 0166-3542; 1872-9096
• DOI: 10.1016/j.antiviral.2006.11.014

SeqHepB is a combination of a HBV genome sequence analysis program and a relational database that houses data collected from multiple data sources. Registered users can access the sequence analysis component of SeqHepB online for rapid and detailed interrogation of HBV genomic sequences. Its main function is to determine the HBV genotype, identify key mutations associated with antiviral resistance, and identify clinically important HBV mutants. All information generated is uploaded into a database and integrated with patient medical records, pathology laboratory tests, and supplemental virology results such as in vitro drug cross-resistance values. Combined with structured query language (SQL) queries developed in the database, it is possible to extract and correlate clinical, virological, and in vitro phenotypic data rapidly and efficiently. An important component of SeqHepB is its ability to integrate mutations detected within the reverse transcriptase (RT) and locate them onto a three-dimensional (3D) model of the HBV RT that can be viewed at any angle with known antiviral drug molecules in the catalytic pocket of the enzyme. SeqHepB will enable virologists and physicians to individualise patient management, cope with the explosion of antiviral associated HBV mutations, and to conduct cross-sectional retrospective or prospective studies on HBV-infected individuals during therapy.