ArticleBioinformatics (Oxford, England)2015
PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed.
- Development and validation of a new mpox virus sequencing and bioinformatic analysis pipeline.Emerging microbes & infections · 2025Article
- Temporal and Spatial Survey on the Abundance of Amoebae and Bacteria in an Estuary and the Role of Environmental Parameters.Environmental microbiology reports · 2025Article
- Environmental diversity ofmSystems · 2025Article
- AutoPVPrimer: A comprehensive AI-Enhanced pipeline for efficient plant virus primer design and assessment.PloS one · 2025Article
- DeGenPrime provides robust primer design and optimization unlocking the biosphere.Bioinformatics advances · 2024Article
- Article
- A tool to automatically design multiplex PCR primer pairs for specific targets using diverse templates.Scientific reports · 2023Article
- Article
- Co-circulation ofFrontiers in microbiology · 2023Article
- Mastadenovirus Molecular Diversity in Waste and Environmental Waters from the Lisbon Metropolitan Area.Microorganisms · 2022Article
- Identifying group-specific primers for environmental Heterolobosa by high-throughput sequencing.Microbial biotechnology · 2022Article
- Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design.Genes & genomics · 2022Article
- Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens.PLOS global public health · 2022Article
- Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia.Microbiology spectrum · 2021Article
- Human Polyomaviruses (HPyV) in Wastewater and Environmental Samples from the Lisbon Metropolitan Area: Detection and Genetic Characterization of Viral Structural Protein-Coding Sequences.Pathogens (Basel, Switzerland) · 2021Article
- The Early Evolution of Oral Poliovirus Vaccine Is Shaped by Strong Positive Selection and Tight Transmission Bottlenecks.Cell host & microbe · 2021Article
- Article
- Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture.Microbial genomics · 2020Article
- Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release.Biotechnology and bioengineering · 2020Article
- NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus.Database : the journal of biological databases and curation · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
summaryAnalyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several options for multiple-primer design, allowing researchers to efficiently design walking primers that cover long DNA targets, such as entire HIV-1 genomes, and that optimizes primers simultaneously informed by genetic diversity in multiple alignments and experimental design constraints given by the user. PrimerDesign-M can also design primers that include DNA barcodes and minimize primer dimerization. PrimerDesign-M finds optimal primers for highly variable DNA targets and facilitates design flexibility by suggesting alternative designs to adapt to experimental conditions. AVAILABILITY AND IMPLEMENTATION: PrimerDesign-M is available as a webtool at http://www.hiv.lanl.gov/content/sequence/PRIMER_DESIGN/primer_design.html CONTACT: tkl@lanl.gov or seq-info@lanl.gov.
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