title: MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments.
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.
authors.affiliation: Department of Information and Communication Engineering, DGIST, Daegu 42988, South Korea.
authors.forename: Hyerin
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, South Korea.
authors.forename: NaNa
authors.initials: N
authors.lastname: Kang
authors.affiliation: Department of Information and Communication Engineering, DGIST, Daegu 42988, South Korea.
authors.forename: KyuHyeon
authors.initials: K
authors.lastname: An
authors.affiliation: Department of Brain and Cognitive Sciences, DGIST, Daegu 42988, South Korea jkoo001@dgist.ac.kr.
authors.forename: JaeHyung
authors.initials: J
authors.lastname: Koo
authors.affiliation: Department of Information and Communication Engineering, DGIST, Daegu 42988, South Korea mskim@dgist.ac.kr.
authors.forename: Min-Soo
authors.initials: MS
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D017931:DNA Primers / Q000138:chemical synthesis / Q000737:chemistry*; D006801:Humans; D020407:Internet; D051379:Mice; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012689:Sequence Homology, Nucleic Acid; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers