Article: SSDPrimer: an SSD-based primer design method for a private sequence DB Journal: International Journal of Data Mining and Bioinformatics (IJDMB) 2017 Vol.18 No.3 pp.252 - 267 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. Inderscience Publishers - linking academia, business and industry through research

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

Authors: Kang-Wook Chon; Sang-Hyun Hwang; Kyuhyeon An; Min-Soo Kim

Addresses: Department of Information and Communication Engineering, DGIST, Daegu, South Korea ' Department of Information and Communication Engineering, DGIST, Daegu, South Korea ' Department of Information and Communication Engineering, DGIST, Daegu, South Korea ' Department of Information and Communication Engineering, DGIST, Daegu, South Korea

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.

Keywords: qPCR; sequence DB; primer design; SSD; single machine; disk-based algorithm; scalable algorithm; genes; molecular biology; software; cloning.

DOI: 10.1504/IJDMB.2017.087186

International Journal of Data Mining and Bioinformatics, 2017 Vol.18 No.3, pp.252 - 267

Received: 07 Jul 2017
Accepted: 26 Jul 2017
Published online: 06 Oct 2017 *

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

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