GLUE: a flexible software system for virus sequence data

• Published in: BMC bioinformatics Vol. 19; no. 1; p. 532
• Main Authors: Singer, Joshua B, Thomson, Emma C, McLauchlan, John, Hughes, Joseph, Gifford, Robert J
• Format: Journal Article
• Language: English
• Published: England BioMed Central 18-12-2018; BMC
• Subjects: Algorithms; Amino Acid Sequence; Annotations; Applications programs; Automation; Base Sequence; Bioinformatics; Biological evolution; Case studies; Computer graphics; Data processing; Drug resistance; Drug Resistance, Viral - genetics; Epidemics; Evolution; Evolutionary genetics; Gene sequencing; Genome, Viral; Genomes; Genotype; Genotype & phenotype; Genotypes; Genotyping; Genotyping Techniques; Hepacivirus - genetics; Hepatitis; Hepatitis C; Hepatology; HIV; Human immunodeficiency virus; Humans; Influenza; Integrated software; Internet; Internet resources; Likelihood Functions; Nucleotide sequence; Outbreaks; Phylogenetics; Public health; Sequence Alignment; Sequence database; Software; Therapeutic applications; Viral Proteins - chemistry; Virology; Virus evolution; Virus genotyping; Virus sequence data; Viruses; Web-based bioinformatics; Virus genotyping; Virus sequence data; Virus evolution; Sequence database; Web-based bioinformatics
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-018-2459-9

Virus genome sequences, generated in ever-higher volumes, can provide new scientific insights and inform our responses to epidemics and outbreaks. To facilitate interpretation, such data must be organised and processed within scalable computing resources that encapsulate virology expertise. GLUE (Genes Linked by Underlying Evolution) is a data-centric bioinformatics environment for building such resources. The GLUE core data schema organises sequence data along evolutionary lines, capturing not only nucleotide data but associated items such as alignments, genotype definitions, genome annotations and motifs. Its flexible design emphasises applicability to different viruses and to diverse needs within research, clinical or public health contexts.
HCV-GLUE is a case study GLUE resource for hepatitis C virus (HCV). It includes an interactive public web application providing sequence analysis in the form of a maximum-likelihood-based genotyping method, antiviral resistance detection and graphical sequence visualisation. HCV sequence data from GenBank is categorised and stored in a large-scale sequence alignment which is accessible via web-based queries. Whereas this web resource provides a range of basic functionality, the underlying GLUE project can also be downloaded and extended by bioinformaticians addressing more advanced questions.
GLUE can be used to rapidly develop virus sequence data resources with public health, research and clinical applications. This streamlined approach, with its focus on reuse, will help realise the full value of virus sequence data.