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MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR

MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR
Kim, HyerinKang, NaNaChon, Kang-WookKim, SeonhoLee, NaHyeKoo, JaeHyungKim, Min-Soo
DGIST Authors
Kang, NaNaKoo, JaeHyungKim, Min-Soo
Issued Date
Article Type
Quantitative AnalysisREFSEQSEQUENCESTHERMODYNAMICSTOOLValidation StudyAnalytical EquipmentArticleComparative StudyControlled StudyDATABASEDEGENERATE PRIMERSDNA DeterminationDNA SequenceDNA StructureDNA SynthesisGENE-EXPRESSION ANALYSISGENOMESHumanHYBRID OLIGONUCLEOTIDE PRIMERSMouseNonhumanNucleic ACID DatabasePOLYMERASE-CHAIN-REACTIONPolymerase Chain ReactionPrimer DNAPriority Journal
Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That approach is inconvenient for many target sequences of quantitative PCR (qPCR) due to considering the same stringent and allele-invariant constraints. To address this issue, we propose an entirely new method called MRPrimer that can design all feasible and valid primer pairs existing in a DNA database at once, while simultaneously checking a multitude of filtering constraints and validating primer specificity. Furthermore, MRPrimer suggests the best primer pair for each target sequence, based on a ranking method. Through qPCR analysis using 343 primer pairs and the corresponding sequencing and comparative analyses, we showed that the primer pairs designed by MRPrimer are very stable and effective for qPCR. In addition, MRPrimer is computationally efficient and scalable and therefore useful for quickly constructing an entire collection of feasible and valid primers for frequently updated databases like RefSeq. Furthermore, we suggest that MRPrimer can be utilized conveniently for experiments requiring primer design, especially real-time qPCR. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Oxford University Press
Related Researcher
  • 구재형 Koo, JaeHyung 뉴바이올로지학과
  • Research Interests 장내미생물/감염균 유래 대사체를 통한 신경염증; 알츠하이머병; 우울증; 당뇨/비만; 대사체/수용체 상호작용에 의한 대사연구
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Department of Electrical Engineering and Computer Science InfoLab 1. Journal Articles
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Department of New Biology Brain-Immune Axis Laboratory 1. Journal Articles


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