ArticlePloS one2012
Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Review
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- Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater.bioRxiv : the preprint server for biology · 2025Article
- Phylogenetic Analysis of Grapevine Fanleaf Virus, Grapevine Virus A, and Grapevine Leafroll-Associated Virus 3 in Kazakhstan.Microorganisms · 2025Article
- Article
- Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets.BMC bioinformatics · 2025Article
- Molecular Assays Versus Mycological Methods for Diagnosis of Rhino Orbital Mucormycosis: Analysis of 120 Clinical Specimens from COVID-19 Patients.Mycopathologia · 2025Article
- Diagnosis of acute Q fever using targeted next‑generation sequencing: A case report.Experimental and therapeutic medicine · 2025Article
- Article
- Lack of abundant core virome inmSystems · 2024Article
- Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes.BMC bioinformatics · 2024Article
- Article
- Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals.eLife · 2023Article
- A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species.Molecular ecology resources · 2022Article
- Prider: multiplexed primer design using linearly scaling approximation of set coverage.BMC bioinformatics · 2022Article
- Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes.BMC evolutionary biology · 2020Article
- AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies.Bioinformatics (Oxford, England) · 2020Article
- Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples.PLoS neglected tropical diseases · 2019Article
- Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype.PLoS neglected tropical diseases · 2018Article
- Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.Nature protocols · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PriMux is a new software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups. PriMux has the capability to predict degenerate primers as well as probes suitable for TaqMan or other primer/probe triplet assay formats, or simply probes for microarray or other single-oligo assay formats. PriMux employs suffix array methods for efficient calculations on oligos 10-~100 nt in length. TaqMan® primers and probes for each segment of Rift Valley fever virus were designed using PriMux, and lab testing comparing signatures designed using PriMux versus those designed using traditional methods demonstrated equivalent or better sensitivity for the PriMux-designed signatures compared to traditional signatures. In addition, we used PriMux to design TaqMan® primers and probes for unalignable or poorly alignable groups of targets: that is, all segments of Rift Valley fever virus analyzed as a single target set of 198 sequences, or all 2863 Dengue virus genomes for all four serotypes available at the time of our analysis. The PriMux software is available as open source from http://sourceforge.net/projects/PriMux.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.