High-density resequencing microarrays produce variable length segments, 10 2 -10 5 bp, of direct sequence information. This target sequence falls in the longer target regime of PCR approaches but rather than being hybridized to a longer lessspecific probe on the microarray, many shorter specific probes are placed on the microarray to allow more detailed determinations from the entire PCR amplicon. This also means that the specificity of the primers used can be relaxed. They have been successfully used to detect single nucleotide polymorphism (SNP) and genetic variants from viral, bacterial and eukaryotic genomes (5) (6) (7) (8) (9) (10) (11) (12) . Their use for SNP detection has clearly established their ability to provide reliable quality sequence information. In most cases, the microarrays were designed to study a limited number of genetically similar target pathogens and for many cases, the detection methods relied only on recognizing hybridization patterns for identification (6, 9, 10, 13, 14) . Taking advantage of the sequential base resolution capability of resequencing microarrays that is required for SNP detection, resequencing has recently been successfully adapted recently using a different approach for organism identification of multiple bacterial and viral pathogens while allowing for fine detailed discrimination of closely related organisms and tracking mutations within the targeted pathogen (15) (16) . The new methodology differed from earlier work by using the resolved bases as the query of a similarity search of DNA databases to identify the most likely species and variants that match the base calls from the hybridization observed. The system was capable of testing for 26 pathogens simultaneously and could detect the presence of multiple pathogens. A software program, resequencing pathogen identifier (REPI), was used to simplify data analysis by performing similarity searches of a genetic database using basic local alignment search tool (BLAST) (17) . The REPI program used BLAST default settings and would only return sequences that might represent the hybridization if the expect value, a quantity calculated by the BLAST program that indicates the likelihood that the sequence match found would have occurred by random chance in the database, was <10 À9 . This screened out all cases that had insufficient signal; however, the final determination of what pathogen(s) was detected and to what degree discrimination was possible required manual examination of the returned results. This method successfully allowed fine discrimination of various adenoviruses and strain identifications of Flu A and B samples in agreement with conventional sampling results (15, 16) . Two important advantages of this approach were that the information was always recovered at the most detailed level possible and that it was capable of still recognizing organisms with recent mutations. This approach also maintained specificity well, as it was not dependent on the uniqueness of a few individual short probes.