Please use this identifier to cite or link to this item: https://doi.org/10.1186/1471-2105-9-368
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dc.titleLOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens
dc.contributor.authorLee, W.H.
dc.contributor.authorWong, C.W.
dc.contributor.authorLeong, W.Y.
dc.contributor.authorMiller, L.D.
dc.contributor.authorSung, W.K.
dc.date.accessioned2013-07-04T07:48:29Z
dc.date.available2013-07-04T07:48:29Z
dc.date.issued2008
dc.identifier.citationLee, W.H., Wong, C.W., Leong, W.Y., Miller, L.D., Sung, W.K. (2008). LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens. BMC Bioinformatics 9. ScholarBank@NUS Repository. https://doi.org/10.1186/1471-2105-9-368
dc.identifier.issn14712105
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/39740
dc.description.abstractBackground: Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals. Results: In this paper, we study how the efficiency of random PCR amplification affects hybridization signals. We describe a model that predicts the amplification efficiency of a given random primer on a target viral genome. The prediction allows us to filter false-negative probes of the genome that lie in regions of poor random PCR amplification and improves the accuracy of pathogen detection. Subsequently, we propose LOMA, an algorithm to generate random primers that have good amplification efficiency. Wet-lab validation showed that the generated random primers improve the amplification efficiency significantly. Conclusion: The blind use of a random primer with attached universal tag (random-tagged primer) in a PCR reaction on a pathogen sample may not lead to a successful amplification. Thus, the design of random-tagged primers is an important consideration when performing PCR. © 2008 Lee et al; licensee BioMed Central Ltd.
dc.description.urihttp://libproxy1.nus.edu.sg/login?url=http://dx.doi.org/10.1186/1471-2105-9-368
dc.sourceScopus
dc.typeArticle
dc.contributor.departmentCOMPUTER SCIENCE
dc.description.doi10.1186/1471-2105-9-368
dc.description.sourcetitleBMC Bioinformatics
dc.description.volume9
dc.description.codenBBMIC
dc.identifier.isiut000259531500001
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