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SSDPrimer: an SSD-based primer design method for a private sequence DB
- SSDPrimer: an SSD-based primer design method for a private sequence DB
- Chon, Kang Wook; Hwang, Sang Hyun; An, Kyu Hyeon; Kim, Min-Soo
- DGIST Authors
- Kim, Min-Soo
- Issue Date
- International Journal of Data Mining and Bioinformatics, 18(3), 252-267
- Article Type
- Cloning; Diskbased Algorithm; Genes; Machine; Molecular Biology; Primer Design; Qpcr; Real Time Polymerase Chain Reaction; Scalable Algorithm; Sequence DB; Single Machine; Software; Ssd; Storage; Velocity; Web Browser
- Many tools and websites have been proposed to help users to design primers for quantitative Polymerase Chain Reaction (qPCR) experiments. Most of these tools and websites require the external step using BLAST-like tools to perform homology tests on off-target sequences for feasible and valid primers. Although MRPrimer tools have been proposed to design primers without the external step, they have drawbacks that they should be performed on a cluster of machine, or only allow users to design their primers on specific sequence DB. However, utilising a cluster of machine is usually expensive, and designing primers on their own private sequence DB is indispensable in many cases. In order to solve the above problems, we propose a new primer design method called SSDPrimer that runs on a single machine, but achieves a comparable speed with the MRPrimer method by exploiting SSD storage. It allows users to design primers on private sequence DBs. In addition, SSDPrimer supports the web browser interface such that users can easily design high-quality primers for target sequences by querying. Copyright © 2017 Inderscience Enterprises Ltd.
- Inderscience Enterprises Ltd.
- Related Researcher
Kim, Min Soo
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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