Summary
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.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Briese, P., Palacios, G., Kokoris, M., Jabado, O., Liu, Z., Renwick, N., Kapoor, V., Casas, I., Pozo, F., Limberger, R. and Lipkin, W. (2005) Diagnostic system for rapid and sensitive differential detection of pathogens. Emerg Infect Dis 11(2), 310–313.
Guilbaud, M., Coppet, P., Bourion, F., Rachman, C. and Dousset, X. (2005) Quantitative detection of Listeria monocytogenes in biofilms by real-time PCR. Appl Environ Microbiol, 2190–2194.
Higgins, D. G. and Sharp, P. M. (1998) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244.
Holland, P. M., Abramson, R. D., Watson, R. and Gelfand D. H. (1991) Detection of specific polymerase chain reaction product by utilizing 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci USA 88, 7276–7280.
Verweij, J. J., Blange R. A., Templeton, K., Schinkel, J., Brienen E. A., van Rooyen, M. A, et al. (2004) Simultaneous detection of Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum in fecal samples by using multiplex real-time PCR. J Clin Microbiol 42, 1220–1223.
Vet J. A., Majithia, A. R., Marras, S.A., Tyagi, S., Dube, S., Poiesz, B.J., et al. (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc Natl Acad Sci USA 96, 6394–6399.
Salvatore, M., Kramer F. R. and Tyagi, S. (1999) Multiplex detection of single-nucleotide variations using molecular beacons. Genet Anal 14, 151–156.
Matveeva, O. V., Foley, B. T., Nemtsov, V. A., et al. (2004) Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. BMC Bioinformatics 5(1), 44–51.
Relman, D. A. (1998) Detection and identification of previously unrecognized microbial pathogens. Emerg Infect dis 4(3), 382–389.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press
About this protocol
Cite this protocol
Apte, A., Singh, S. (2007). AlleleID. In: Yuryev, A. (eds) PCR Primer Design. Methods in Molecular Biology™, vol 402. Humana Press. https://doi.org/10.1007/978-1-59745-528-2_17
Download citation
DOI: https://doi.org/10.1007/978-1-59745-528-2_17
Publisher Name: Humana Press
Print ISBN: 978-1-58829-725-9
Online ISBN: 978-1-59745-528-2
eBook Packages: Springer Protocols