Efficient oligonucleotide probe selection for pan-genomic tiling arrays |
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Authors: | Adam M Phillippy Xiangyu Deng Wei Zhang Steven L Salzberg |
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Affiliation: | (1) Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA;(2) National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, IL 60501, USA |
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Abstract: | Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray applications, requires adequate coverage of probes targeting the regions of interest. An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. However, such a whole-genome tiling requires that the genome sequence is known in advance. For the accurate analysis of uncharacterized bacteria, an array must query a fully representative set of sequences from the species' pan-genome. Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome. |
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