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.
Subject(s)
Computational Biology/methods , Virology/methods , Virus Physiological Phenomena , Viruses/genetics , Genotype , PhenotypeSubject(s)
Antimetabolites/pharmacology , Psoriasis/drug therapy , Skin/drug effects , Animals , Anthralin/pharmacology , Azauridine/pharmacology , Cell Division/drug effects , Cells, Cultured , Cycloheximide/pharmacology , Cytarabine/pharmacology , Dactinomycin/pharmacology , Daunorubicin/pharmacology , Guinea Pigs , Hydroxyurea/pharmacology , Methotrexate/pharmacology , Mycophenolic Acid/pharmacology , Puromycin/pharmacology , Skin/cytologyABSTRACT
The phenomenon of selective translation of T4 template RNA by ribosomes from T4-infected cells, or factors derived therefrom, has been extended to studies on the initiation of protein synthesis. A high-salt extract derived from T4-infected ribosomes inhibits the formation of initiation complexes of MS2 and Escherichia coli template RNA with uninfected ribosomes while efficiently supporting the formation of initiation complexes with T4 template RNA. T4 factors also permit T5 template RNA to bind to E. coli ribosomes, which indicates that the T4 selective effect is not exclusive for T4 templates. Other evidence indicates that T4 factors do not alter the process of polypeptide chain elongation.
