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MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments

MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments
Kim, H[Kim, Hyerin]Kang, N[Kang, NaNa]An, K[An, KyuHyeon]Koo, J[Koo, JaeHyung]Kim, MS[Kim, Min-Soo]
DGIST Authors
Kim, H[Kim, Hyerin]; Kang, N[Kang, NaNa]; An, K[An, KyuHyeon]; Koo, J[Koo, JaeHyung]Kim, MS[Kim, Min-Soo]
Issue Date
Nucleic Acids Research, 44(W1), W259-W266
Article Type
Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access:
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)
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