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.

本描述了一种定制的FMDV微阵列及其配套的功能与模板辅助组装软件（FAT-组装器），该软件能够利用一定数量的保守微阵列特征解析病毒基因组序列。研究结果表明，该方法可用于快速表征自然发生的FMDV及其工程化的嵌合病毒株。尽管FAT-组装器主要用于解析FMDV基因组，但其代表了一种新的生物信息学方法，该方法应广泛应用于解读其他病毒或目标生物的微阵列基因分型数据。总体设计：对代表七个血清型的七个口蹄疫病毒田间分离株以及一个单一生成的嵌合株进行了总核酸提取，随后进行核酸扩增和荧光标记。标记的核酸与Agilent（8x60K）定制微阵列（Agilent-033126）杂交，并使用GenePix软件进行扫描。原始GPR文件的输出随后通过特征和模板辅助组装软件进行处理，以生成共识序列，并将其与已知序列进行比较，以确定算法的准确性。