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SSDPrimer: an SSD-based primer design method for a private sequence DB

Title
SSDPrimer: an SSD-based primer design method for a private sequence DB
Authors
Chon, Kang WookHwang, Sang HyunAn, Kyu HyeonKim, Min-Soo
DGIST Authors
Chon, Kang Wook; Hwang, Sang Hyun; An, Kyu Hyeon; Kim, Min-Soo
Issue Date
2017
Citation
International Journal of Data Mining and Bioinformatics, 18(3), 252-267
Type
Article
Article Type
Article
Keywords
CloningDiskbased AlgorithmGenesMachineMolecular BiologyPrimer DesignQpcrReal Time Polymerase Chain ReactionScalable AlgorithmSequence DBSingle MachineSoftwareSsdStorageVelocityWeb Browser
ISSN
1748-5673
Abstract
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.
URI
http://hdl.handle.net/20.500.11750/4709
DOI
10.1504/IJDMB.2017.087186
Publisher
Inderscience Enterprises Ltd.
Related Researcher
Files:
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Collection:
Information and Communication EngineeringInfoLab1. Journal Articles


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