Re-sequencing pathogen microarray

A method comprising:

• providing a resequencing DNA microarray;
• contacting an unknown sample comprising genetic material to the resequencing DNA microarray;
• wherein the resequencing DNA microarray comprises multiple groups of oligonucleotide probes of a length ranging from 13 to 70 nucleotides immobilized to a solid phase support;
• wherein each group of oligonucleotide probes is selected to span a region of a reference sequence that is a single gene or subsequence that represents a genus, species, or subspecies of organisms;
• wherein the reference sequence is a consensus sequence that is not identical to any sequence in the genus, species, or subspecies of organisms;
• wherein each group of oligonucleotide probes occupies a tiled region of the microarray;
• wherein each group of oligonucleotide probes comprises at least four probes arranged in a parallel fashion within the tiled region of the array, wherein the four probes are selected as follows:
• i) a first probe that is exactly complementary to the reference sequence;
• and
• ii) three additional probes, each of which is identical to the first probe but for the nucleotide at a central position, which is different in each of the three additional probes such that all four nucleotide bases are present on the microarray;
• hybridizing a nucleic acid in the unknown sample to the resequencing DNA microarray;
• generating a sequence of base calls based on a hybridization response between the nucleic acid in the unknown sample and the probes on the resequencing DNA microarray;
• and
• determining the sequence of a full-length gene or genomic fragment corresponding to the nucleic acid in the unknown sample by comparing the sequence of base calls to a sequence database containing sequences from the genus, species, or subspecies of organisms.