MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments

Kim, Hyerin; Kang, NaNa; An, Kyuhyeon; Koo, Jae Hyung; Kim, Min‐Soo

doi:10.1093/nar/gkw380

Cited by 15 publications

(13 citation statements)

References 22 publications

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“…After computation, the workflow generated a total of 51 091 785 gene-specific qPCR primer pairs, corresponding to 93.4% of the average coverage ratios, per organism, and an average of 15.3 primer pairs per gene (Table 1 and Supplementary Table S1 ). In human and mouse, more than 19 and 22 primer pairs, per gene, were obtained, with a coverage ratio of 78.8 and 90.3%, respectively ( Supplementary Table S1 ), indicating that the results of our workflow are in accordance with those in MRPrimerW ( 15 ) and PrimerBank ( 16 ). Moreover, it is more difficult to design qPCR primers for plants than for animals.…”

Section: Methodssupporting

confidence: 54%

“…Although these programs have been optimized, it is still difficult for most researchers to design many qPCR primers that simultaneously satisfy the requirements for stringent, uniform amplification conditions. Therefore, various qPCR primer databases have been developed to provide pre-designed, specific qPCR primers, such as AtRTPrimer ( 13 ), GETPrime 2.0 ( 14 ), MRPrimerW ( 15 ), PrimerBank ( 16 ), qPrimerDepot ( 17 ) and RTPrimerDB ( 18 ). Unfortunately, these databases were designed based on only a few important organisms.…”

Section: Introductionmentioning

confidence: 99%

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qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms

Tian

et al. 2017

Nucleic Acids Research

120

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Real-time quantitative polymerase chain reaction (qPCR) is one of the most important methods for analyzing the expression patterns of target genes. However, successful qPCR experiments rely heavily on the use of high-quality primers. Various qPCR primer databases have been developed to address this issue, but these databases target only a few important organisms. Here, we developed the qPrimerDB database, founded on an automatic gene-specific qPCR primer design and thermodynamics-based validation workflow. The qPrimerDB database is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 147 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice and maize. In this database, we provide 3331426 of the best primer pairs for each gene, based on primer pair coverage, as well as 47760359 alternative gene-specific primer pairs, which can be conveniently batch downloaded. The specificity and efficiency was validated for qPCR primer pairs for 66 randomly selected genes, in six different organisms, through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be routinely updated, is publically accessible at http://biodb.swu.edu.cn/qprimerdb.

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Section: Methodssupporting

confidence: 54%

Section: Introductionmentioning

confidence: 99%

qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms

Tian

et al. 2017

Nucleic Acids Research

120

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“…The comparison to the most renowned databases, RTPrimerDB [ 15 ], GETPrime 2.0 [ 8 ], qPrimerDB [ 9 ], PrimerBank [ 5 ] and MrPrimerW [ 16 ] is summarised in Table 3 .…”

Section: Resultsmentioning

confidence: 99%

PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization

Burger¹,

Angioni²,

Russo³

et al. 2018

BMC Bioinformatics

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BackgroundPrimer design is a crucial step in establishing specific and sensitive qPCR assays. Even though numerous tools for primer design exist, the majority of resulting assays still requires extensive testing and optimisation or does not allow for high quality target amplification. We developed a workflow for designing qPCR assays. Unlike other tools, we compute a PCR assay including primer design, concentrations and the optimal PCR program.ResultsGene expression assays were already generated in a total of 283,226 genes from three species and are continued for all genes of the major model species. The results are available online at https://pcrdrive.com/lab#/assay-database. The workflow involves filtering Primer3-generated primers by considering diverse parameters including specificity, single-nucleotide polymorphisms (SNPs), secondary structure as well as compatibility with standard qPCR assay conditions. The resulting assays consist of transcript-specific primer sequences, a reagents protocol as well as instrument settings which are provided in a web-based tool called PCRdrive. PCRdrive was designed to support PCR users in their PCR-related tasks and is equipped with handy functions, components of an electronic lab notebook (ELN) as well as teamworking opportunities.ConclusionHigh quality ready to use qPCR assays for gene expression analysis are provided within the online platform PCRdrive. A built-in primer designer enables easy generation of assays which is not supported by any other tool. The wet lab optimisation of new assays can be transparently documented and shared within the team. PCRdrive also contains an archive of public PCRs which is updated regularly. Users may use the archive to publish their PCR to the community which makes it easy for other researchers worldwide to reproduce and validate the PCR. PCRdrive is a growing network of PCR users, simplifying and streamlining research through its useful existing features and continuous developments from the active development team.

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“…Many websites have been developed to aid in designing primers for qPCR, including Primer3Plus (6,7), BatchPrimer3 (8), Primique (9), QuantPrime (10), Primer-BLAST (11), Oli2go (12) and MRPrimerW (13). There are also many databases containing pre-computed primers, including PrimerBank (14,15) and qPrimerDB (16).…”

Section: Introductionmentioning

confidence: 99%

“…MRPrimerW (13) is our previously proposed website which allows users to quickly search for the best valid primer pairs satisfying the same constraints for many target sequences. It extracted a complete set of 341 963 135 valid primers which can amplify only a specific sequence from the human and mouse CCDS databases (https://www.ncbi.nlm.nih.gov/CCDS/) in an exhaustive manner using the large-scale MapReduce program called MRPrimer (18), converted them to a set of indices with annotations, and loaded into the main memory of the website.…”

Section: Introductionmentioning

confidence: 99%

MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments

Jeon

Bae

Hwang

et al. 2019

Nucleic Acids Research

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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

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MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments

Cited by 15 publications

References 22 publications

qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms

qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms

PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization

MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments

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