1. MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments
- Author
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Hyun Seob Lee, Sang Hyun Hwang, Hyerin Kim, Hajin Jeon, Min-Soo Kim, Jeongmin Bae, and Kyu-Young Whang
- Subjects
Sequence analysis ,Single pair ,Computational biology ,Biology ,Real-Time Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Software ,Genetics ,Animals ,Humans ,DNA Primers ,030304 developmental biology ,PCI Express ,0303 health sciences ,business.industry ,Free access ,Exons ,Rats ,Web Server Issue ,Cattle ,Primer (molecular biology) ,business ,Sequence Analysis ,030217 neurology & neurosurgery - Abstract
For the best results in quantitative polymerase chain reaction (qPCR) experiments, it is essential to design high-quality primers considering a multitude of constraints and the purpose of experiments. The constraints include many filtering constraints, homology test on a huge number of off-target sequences, the same constraints for batch design of primers, exon spanning, and avoiding single nucleotide polymorphism (SNP) sites. The target sequences are either in database or given as FASTA sequences, and the experiment is for amplifying either each target sequence with each corresponding primer pairs designed under the same constraints or all target sequences with a single pair of primers. Many websites have been proposed, but none of them including our previous MRPrimerW fulfilled all the above features. Here, we describe the MRPrimerW2, the update version of MRPrimerW, which fulfils all the features by maintaining the advantages of MRPrimerW in terms of the kinds and sizes of databases for valid primers and the number of search modes. To achieve it, we exploited GPU computation and a disk-based key-value store using PCIe SSD. The complete set of 3 509 244 680 valid primers of MRPrimerW2 covers 99% of nine important organisms in an exhaustive manner. Free access: http://MRPrimerW2.com
- Published
- 2019