Cited 6 time in webofscience Cited 5 time in scopus

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, H[Kim, Hyerin]Kang, N[Kang, NaNa]Chon, KW[Chon, Kang-Wook]Kim, S[Kim, Seonho]Lee, N[Lee, NaHye]Koo, J[Koo, JaeHyung]Kim, MS[Kim, Min-Soo]
DGIST Authors
Kim, H[Kim, Hyerin]; Kang, N[Kang, NaNa]; Chon, KW[Chon, Kang-Wook]; Kim, S[Kim, Seonho]; Lee, N[Lee, NaHye]; Koo, J[Koo, JaeHyung]Kim, MS[Kim, Min-Soo]
Issue Date
Nucleic Acids Research, 43(20)
Article Type
Analytical EquipmentComparative StudyControlled StudyDNA DeterminationDNA SequenceDNA StructureDNA SynthesisHumanMouseNon-HumanNucleic Acid DatabasePolymerase Chain ReactionPrimer DNAPriority JournalQuantitative AnalysisValidation Study
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
  • Author Kim, Min-Soo InfoLab
  • Research Interests Big Data Systems; Big Data Mining & Machine Learning; Big Data Bioinformatics; 데이터 마이닝 및 빅데이터 분석; 바이오인포메틱스 및 뉴로인포메틱스; 뇌-기계 인터페이스(BMI)
There are no files associated with this item.
Department of Brain and Cognitive SciencesMolecular & Cellular Smell Biology Lab1. Journal Articles
Department of Information and Communication EngineeringInfoLab1. Journal Articles

qrcode mendeley

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.