ArticleBMC bioinformatics2013
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Genome-wide discovery of short sequence repeat markers useful for genetic diversity studies in Lima bean (Phaseolus lunatus L.).Scientific reports · 2025Article
- Development and validation of a new mpox virus sequencing and bioinformatic analysis pipeline.Emerging microbes & infections · 2025Article
- Model-directed generation of artificial CRISPR-Cas13a guide RNA sequences improves nucleic acid detection.Nature biotechnology · 2025Article
- Laboratory validation of targeted next-generation sequencing assay for pathogen detection in lower respiratory infection.Microbiology spectrum · 2025Article
- Article
- Designing sensitive viral diagnostics with machine learning.Nature biotechnology · 2022Article
- rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses.BMC bioinformatics · 2022Article
- Prider: multiplexed primer design using linearly scaling approximation of set coverage.BMC bioinformatics · 2022Article
- Infection of Human Retinal Pigment Epithelial Cells with Dengue Virus Strains Isolated during Outbreaks in Singapore.Microorganisms · 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
- VariantStore: an index for large-scale genomic variant search.Genome biology · 2021Article
- Blocking Formation of the Stable HIV Reservoir: A New Perspective for HIV-1 Cure.Frontiers in immunology · 2019Review
- Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene.BMC bioinformatics · 2018Article
- Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia.Applications in plant sciences · 2018Review
- PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection.Scientific reports · 2016Article
- Article
- Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants.Viruses · 2015Observational
- PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes.Bioinformatics (Oxford, England) · 2015Article
- BLASTPLOT: a PERL module to plot next generation sequencing NCBI-BLAST results.Source code for biology and medicine · 2014Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundPrimer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design.
resultsDesign constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations.
conclusionsPrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples.
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