AlleleID: a pathogen detection and identification system.

Efficient clinical diagnosis of pathogens is important for the management of infectious diseases. Conventional methods have longer turnaround time and, in most cases, lower sensitivity. Nucleic acid-based methods for the detection of microorganisms are rapid, sensitive and are generally successful even when the culturing of microorganisms fails. Sequence-based molecular methods such as real-time PCR, microarrays, and band biosensors provide high sensitivity, rapid diagnostics, and higher specificity allowing differentiation between related strains. Although numerous chemistries are available for the molecular level identification of pathogens, the most common are qPCR and DNA microarrays. Both of these techniques have a high accuracy when used with specific primers and probes. Manual design of these primer and probes is both tedious and results in lower quality of results because of the inability to simultaneously handle multiple criteria for design. Here, we describe a program AlleleID that designs qPCR and microarray assays to identify and detect pathogens.