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

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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.
Publisher
OXFORD UNIV PRESS
Issue Date
2016-07
Language
English
Article Type
Article
Citation

NUCLEIC ACIDS RESEARCH, v.44, no.W1, pp.W259 - W266

ISSN
0305-1048
DOI
10.1093/nar/gkw380
URI
http://hdl.handle.net/10203/272813
Appears in Collection
CS-Journal Papers(저널논문)
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