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Cited by 20Genomics and Phylogenetic StudiesMolecular Biology Techniques and Applicationsvaccines and immunoinformatics approaches

Multiplex primer prediction software for divergent targets

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Gardner, Shea N., Hiddessen, Amy L., Williams, Peter L., Hara, Christine, Wagner, Mark C., Colston, Bill W.·2009·Nucleic Acids Research
DOI 10.1093/nar/gkp659PMC PMC2770652
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Abstract

We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ( approximately 3700 18-mers or approximately 2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus.

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  • Studies focusing on closely related species may benefit from algorithms that excel at aligning highly similar sequences, while studies on divergent species may require algorithms that can handle high levels of sequence divergence.

    “For instance, studies focusing on closely related species may benefit from algorithms that excel at aligning highly similar sequences, while studies on divergent species may require algorithms that can handle high levels of sequence divergence [63,64].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [64]

    The Introduction (page unavailable) says multiple sequence alignments can be difficult to construct for divergent targets, supporting the need to account for sequence divergence. But the paper addresses primer-design software, not a choice between alignment algorithms for closely related and divergent species; it does not establish the claimed benefit for closely related species. (LLM, conf=0.83)

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Cited by

Sorted by citations

Authors
Gardner, S. N., Hiddessen, A. L., Williams, P. L., Hara, C., Wagner, M. C., & Colston, B. W.
Affiliations
Lawrence Livermore National Laboratory (US)
Corresponding author
  • Gardner, Shea N.
  • Hiddessen, Amy L.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2009-09-16
Volume
37
Issue
19
Pages
6291-6304
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkp659
PMC
PMC2770652
OpenAlex
W2144336920
Cited by
20
References
0
Citations by year
2026: 1 · 2024: 1 · 2023: 3 · 2020: 1 · 2019: 1 · 2015: 3 · 2014: 3 · 2013: 2 · 2012: 2
FWCI
0.63
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, other-oa)
Funders
  • U.S. Department of Energy (DEAC5207NA27344, AC52‐07NA27344)
  • Laboratory Directed Research and Development (DE- AC52-07NA27344, AC52-07NA27344)
  • Lawrence Livermore National Laboratory (DE‐AC5207NA27344, 07NA27344, DE-AC52, AC52-07NA27344)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords
virus detection, foot-and-mouth disease virus, Norwalk virus, HIV-1, poxvirus, vaccinia virus, multiplex PCR
MeSH terms
Algorithms, DNA, Humans, RNA Viruses, Software, Vaccinia virus, Viruses, Sequence Analysis, DNA, DNA Primers

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