Metadata-driven comparative analysis tool for sequences (meta-CATS): An automated process for identifying significant sequence variations that correlate with virus attributes
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Gehrke_Metadata-driven.pdf
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Author(s)
Pickett, B. E.
Liu, M.
Sadat, E. L.
Squires, R. B.
Noronha, J. M.
He, S.
Jen, W.
Zaremba, S.
Gu, Z.
Zhou, L.
Date Issued
December 2013
Journal
Virology
Publisher
Elsevier
Citation
Pickett, B.E., M. Liu, E.L. Sadat, R.B. Squires, J.M. Noronha, S. He, W. Jen, et al. “Metadata-Driven Comparative Analysis Tool for Sequences (meta-CATS): An Automated Process for Identifying Significant Sequence Variations That Correlate with Virus Attributes.” Virology 447, no. 1–2 (December 2013): 45–51. © 2013 Elsevier Inc.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Institute for Medical Engineering & Science
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Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
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DOI of Published Version
https://doi.org/10.1016/j.virol.2013.08.021
