title: Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes.
abstract: The Virus Pathogen Resource (ViPR; www.viprbrc.org) and Influenza Research Database (IRD; www.fludb.org) have developed a metadata-driven Comparative Analysis Tool for Sequences (meta-CATS), which performs statistical comparative analyses of nucleotide and amino acid sequence data to identify correlations between sequence variations and virus attributes (metadata). Meta-CATS guides users through: selecting a set of nucleotide or protein sequences; dividing them into multiple groups based on any associated metadata attribute (e.g. isolation location, host species); performing a statistical test at each aligned position; and identifying all residues that significantly differ between the groups. As proofs of concept, we have used meta-CATS to identify sequence biomarkers associated with dengue viruses isolated from different hemispheres, and to identify variations in the NS1 protein that are unique to each of the 4 dengue serotypes. Meta-CATS is made freely available to virology researchers to identify genotype-phenotype correlations for development of improved vaccines, diagnostics, and therapeutics.
authors.affiliation: J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA 92121, USA. Electronic address: bpickett@jcvi.org.
authors.forename: B E
authors.initials: BE
authors.lastname: Pickett
authors.forename: M
authors.initials: M
authors.lastname: Liu
authors.forename: E L
authors.initials: EL
authors.lastname: Sadat
authors.forename: R B
authors.initials: RB
authors.lastname: Squires
authors.forename: J M
authors.initials: JM
authors.lastname: Noronha
authors.forename: S
authors.initials: S
authors.lastname: He
authors.forename: W
authors.initials: W
authors.lastname: Jen
authors.forename: S
authors.initials: S
authors.lastname: Zaremba
authors.forename: Z
authors.initials: Z
authors.lastname: Gu
authors.forename: L
authors.initials: L
authors.lastname: Zhou
authors.forename: C N
authors.initials: CN
authors.lastname: Larsen
authors.forename: I
authors.initials: I
authors.lastname: Bosch
authors.forename: L
authors.initials: L
authors.lastname: Gehrke
authors.forename: M
authors.initials: M
authors.lastname: McGee
authors.forename: E B
authors.initials: EB
authors.lastname: Klem
authors.forename: R H
authors.initials: RH
authors.lastname: Scheuermann
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005838:Genotype; D010641:Phenotype; D014773:Virology / Q000379:methods*; D018406:Virus Physiological Phenomena; D014780:Viruses / Q000235:genetics*
keywords: Bioinformatics; Comparative genomics; DENV; Database; Dengue; Statistical comparison; Virology; Virus