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PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design

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PCR Primer Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1275))

Abstract

Highly specific and efficient primer and probe design has been a major hurdle in many high-throughput techniques. Successful implementation of any PCR or probe hybridization technique depends on the quality of primers and probes used in terms of their specificity and cross-hybridization. Here we describe PRIMEGENSw3, a set of web-based utilities for high-throughput primer and probe design. These utilities allow users to select genomic regions and to design primer/probe for selected regions in an interactive, user-friendly, and automatic fashion. The system runs the PRIMEGENS algorithm in the back-end on the high-performance server with the stored genomic database or user-provided custom database for cross-hybridization check. Cross-hybridization is checked not only using BLAST but also by checking mismatch positions and energy calculation of potential hybridization hits. The results can be visualized online and also can be downloaded. The average success rate of primer design using PRIMEGENSw3 is ~90 %. The web server also supports primer design for methylated sequences, which is used in epigenetic studies. Stand-alone version of the software is also available for download at the website.

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Acknowledgements

This work has been supported by National Institute of Health (Grant 1R01-DA025779) and the Congressionally Directed Medical Research Programs, U.S. Army Medical Research and Materiel Command (Grant BC062135). This research is also supported in part by the Paul K. and Diane Shumaker Endowment in Bioinformatics.

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Authors and Affiliations

  1. Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA

    Garima Kushwaha

  2. Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA

    Gyan Prakash Srivastava

  3. Computer Science Department, Informatics Institute, and Christopher S. Bond Life Sciences Center, University of Missouri, Office 201 Engineering Building West, Columbia, MO, 65211, USA

    Dong Xu

Authors
  1. Garima Kushwaha
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  2. Gyan Prakash Srivastava
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  3. Dong Xu
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Corresponding author

Correspondence to Dong Xu .

Editor information

Editors and Affiliations

  1. Department of Biology, California State University, Northridge, Los Angeles, California, USA

    Chhandak Basu

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Kushwaha, G., Srivastava, G.P., Xu, D. (2015). PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design. In: Basu, C. (eds) PCR Primer Design. Methods in Molecular Biology, vol 1275. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2365-6_14

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  • DOI: https://doi.org/10.1007/978-1-4939-2365-6_14

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2364-9

  • Online ISBN: 978-1-4939-2365-6

  • eBook Packages: Springer Protocols

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