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

Title
MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments
Authors
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
2016-07-08
Citation
Nucleic Acids Research, 44(W1), W259-W266
Type
Article
Article Type
Article
ISSN
0305-1048
Abstract
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: http://MRPrimerW.com.
URI
http://hdl.handle.net/20.500.11750/2240
DOI
10.1093/nar/gkw380
Publisher
Oxford University Press
Related Researcher
  • Author   InfoLab
  • Research Interests
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Collection:
Department of Brain and Cognitive SciencesMolecular & Cellular Smell Biology Lab1. Journal Articles
Department of Information and Communication EngineeringInfoLab1. Journal Articles


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