title: Development of a Feature and Template-Assisted Assembler and Application to the Analysis of a Foot-and-Mouth Disease Virus Genotyping Microarray.
abstract: Several RT-PCR and genome sequencing strategies exist for the resolution of Foot-and-Mouth Disease virus (FMDV). While these approaches are relatively straightforward, they can be vulnerable to failure due to the unpredictable nature of FMDV genome sequence variations. Sequence independent single primer amplification (SISPA) followed by genotyping microarray offers an attractive unbiased approach to FMDV characterization. Here we describe a custom FMDV microarray and a companion feature and template-assisted assembler software (FAT-assembler) capable of resolving virus genome sequence using a moderate number of conserved microarray features. The results demonstrate that this approach may be used to rapidly characterize naturally occurring FMDV as well as an engineered chimeric strain of FMDV. The FAT-assembler, while applied to resolving FMDV genomes, represents a new bioinformatics approach that should be broadly applicable to interpreting microarray genotyping data for other viruses or target organisms.
authors.affiliation: United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Orient, NY, United States of America.
authors.forename: Roger W
authors.identifier: 0000-0002-4355-0286
authors.initials: RW
authors.lastname: Barrette
authors.affiliation: Department of Environmental and Global Health, Emerging Pathogens Institute University of Florida, Gainesville, FL, United States of America.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Rowland
authors.affiliation: United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Orient, NY, United States of America.
authors.forename: Frederic R
authors.initials: FR
authors.lastname: Grau
authors.affiliation: United States Department of Agriculture, Animal and Plant Health Inspection Service, Foreign Animal Disease Diagnostic Laboratory, Plum Island Animal Disease Center, Orient, NY, United States of America.
authors.forename: Michael T
authors.initials: MT
authors.lastname: McIntosh
mesh_terms: D000465:Algorithms; D002213:Capsid / Q000378:metabolism; D019295:Computational Biology; D017931:DNA Primers; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics*; D016679:Genome, Viral; D005838:Genotype; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D012367:RNA, Viral / Q000235:genetics; D012984:Software
chemical_list: D017931:DNA Primers; D012367:RNA, Viral