Raw microarray derived data for evaluation of a feature and template-assisted assembler for the analysis of foot-and-mouth disease virus by sequence assembly

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 Overall design: Seven field isolates of Foot-and-Mouth Disease virus, representing each of seven serotypes, as well as a single chimeric strain were subject to total nucleic acid extraction, and subsequent nucleic acid amplification, and fluorescent labeling. Labeled nucleic acid was hybridized to Agilent (8x60K) custom microarrays (Agilent-033126) and scanned using GenePix software. The output of the raw GPR file was then passed through the feature and template assisted assembler software for producing consensus sequence which was then compared to the known sequence for determination of accuracy of the algorithm.