MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR Article Swipe
Hyerin Kim
,
NaNa Kang
,
Kang-Wook Chon
,
Seonho Kim
,
NaHye Lee
,
JaeHyung Koo
,
Min‐Soo Kim
·
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkv632
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkv632
Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That approach is inconvenient for many target sequences of quantitative PCR (qPCR) due to considering the same stringent and allele-invariant constraints. To address this issue, we propose an entirely new method called MRPrimer that can design all feasible and valid primer pairs existing in a DNA database at once, while simultaneously checking a multitude of filtering constraints and validating primer specificity. Furthermore, MRPrimer suggests the best primer pair for each target sequence, based on a ranking method. Through qPCR analysis using 343 primer pairs and the corresponding sequencing and comparative analyses, we showed that the primer pairs designed by MRPrimer are very stable and effective for qPCR. In addition, MRPrimer is computationally efficient and scalable and therefore useful for quickly constructing an entire collection of feasible and valid primers for frequently updated databases like RefSeq. Furthermore, we suggest that MRPrimer can be utilized conveniently for experiments requiring primer design, especially real-time qPCR.
Related Topics
Concepts
Primer (cosmetics)
Biology
Primer dimer
Computational biology
RefSeq
Computer science
In silico PCR
Ranking (information retrieval)
Polymerase chain reaction
Scalability
Data mining
Genetics
Multiplex polymerase chain reaction
Database
Information retrieval
Genome
Gene
Organic chemistry
Chemistry
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkv632
- https://academic.oup.com/nar/article-pdf/43/20/e130/16660396/gkv632.pdf
- OA Status
- gold
- Cited By
- 14
- References
- 42
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W1528823460
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W1528823460Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/nar/gkv632Digital Object Identifier
- Title
-
MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCRWork title
- Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2015Year of publication
- Publication date
-
2015-06-24Full publication date if available
- Authors
-
Hyerin Kim, NaNa Kang, Kang-Wook Chon, Seonho Kim, NaHye Lee, JaeHyung Koo, Min‐Soo KimList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gkv632Publisher landing page
- PDF URL
-
https://academic.oup.com/nar/article-pdf/43/20/e130/16660396/gkv632.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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https://academic.oup.com/nar/article-pdf/43/20/e130/16660396/gkv632.pdfDirect OA link when available
- Concepts
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Primer (cosmetics), Biology, Primer dimer, Computational biology, RefSeq, Computer science, In silico PCR, Ranking (information retrieval), Polymerase chain reaction, Scalability, Data mining, Genetics, Multiplex polymerase chain reaction, Database, Information retrieval, Genome, Gene, Organic chemistry, ChemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
14Total citation count in OpenAlex
- Citations by year (recent)
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2021: 4, 2020: 2, 2019: 2, 2017: 3, 2016: 3Per-year citation counts (last 5 years)
- References (count)
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42Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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