tetano
Editor, Senior Moderator
Virology. 2013 Dec;447(1-2):45-51. doi: 10.1016/j.virol.2013.08.021. Epub 2013 Sep 14.
Metadata-driven comparative analysis tool for sequences (meta-CATS): An automated process for identifying significant sequence variations that correlate with virus attributes.
Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, Jen W, Zaremba S, Gu Z, Zhou L, Larsen CN, Bosch I, Gehrke L, McGee M, Klem EB, Scheuermann RH.
Source
J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA 92121, USA. Electronic address: bpickett@jcvi.org.
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.
? 2013 Elsevier Inc. All rights reserved.
KEYWORDS:
Bioinformatics, Comparative genomics, DENV, Database, Dengue, Statistical comparison, Virology, Virus
PMID:
24210098
[PubMed - in process]
http://www.ncbi.nlm.nih.gov/pubmed/24210098
Metadata-driven comparative analysis tool for sequences (meta-CATS): An automated process for identifying significant sequence variations that correlate with virus attributes.
Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, Jen W, Zaremba S, Gu Z, Zhou L, Larsen CN, Bosch I, Gehrke L, McGee M, Klem EB, Scheuermann RH.
Source
J. Craig Venter Institute, 10355 Science Center Drive, San Diego, CA 92121, USA. Electronic address: bpickett@jcvi.org.
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.
? 2013 Elsevier Inc. All rights reserved.
KEYWORDS:
Bioinformatics, Comparative genomics, DENV, Database, Dengue, Statistical comparison, Virology, Virus
PMID:
24210098
[PubMed - in process]
http://www.ncbi.nlm.nih.gov/pubmed/24210098