Статья

Primer3—new capabilities and interfaces

Andreas UntergasserZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, GermanyIoana CutcutacheZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany, 2Neurobiology and Behavioral Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, 3Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia, 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 5Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USATriinu KõressaarZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany, 2Neurobiology and Behavioral Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, 3Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia, 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 5Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USAJian YeZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany, 2Neurobiology and Behavioral Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, 3Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia, 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 5Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USABrant C. FairclothZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany, 2Neurobiology and Behavioral Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, 3Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia, 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 5Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USAMaido RemmZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany, 2Neurobiology and Behavioral Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, 3Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia, 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 5Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USASteve RozenZentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany, 2Neurobiology and Behavioral Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, 3Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia, 4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 5Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA

2012en

ABI

Аннотация

Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3's functionality. In this article, we describe Primer3's current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement-a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.

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Идентификаторы

DOI: 10.1093/nar/gks596

Цитирования и источники

Цитирований: 4Использованных источников: 0

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