期刊
NUCLEIC ACIDS RESEARCH
卷 44, 期 W1, 页码 W259-W266出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw380
关键词
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资金
- Korean Health Technology R&D Project, Ministry for Health, Welfare Family Affairs [HI13C0423]
- DGIST R&D Program of the Ministry of Science, ICT & Technology of Korea [16-BD-06, 16-BD-0404]
- IT R&D program of MSIP/KEIT [Self-Organized Software platform(SoSp) for Welfare Devices] [10041145]
- Ministry of Science, ICT & Future Planning, Republic of Korea [16-BD-06] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
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.
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