ArticleBioinformatics (Oxford, England)2017
RUCS: rapid identification of PCR primers for unique core sequences.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 53 citations in OpenAlex.
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- Tracing of streptococcal strains from infant stools across human body sites links site-specific prevalence to adhesins.Applied and environmental microbiology · 2025Article
- Development of a multi-targeted real-time PCR assay for the detection of the grapevine pathogen Xylophilus ampelinus.Plant methods · 2025Article
- Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing.PLoS neglected tropical diseases · 2025Article
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- Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses.BMC microbiology · 2024Article
- A Rapid and Inexpensive PCR Test for Mastitis Diagnosis Based on NGS Data.Pathogens (Basel, Switzerland) · 2024Article
- Monitoring the growth dynamics of Tetragenococcus halophilus strains in lupine moromi fermentation using a multiplex-PCR system.BMC research notes · 2023Article
- Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data.Journal of clinical microbiology · 2023Article
- Atopic dermatitis-derivedFrontiers in cellular and infection microbiology · 2023Article
- Retrospective survey ofFrontiers in microbiology · 2023Article
- Single Nucleotide Polymorphism-Based Real-Time PCR Screening Assay for Rapid Tracking of Bacterial Infection Clusters To Complement Whole-Genome Sequencing Efforts during Outbreak Investigations.Microbiology spectrum · 2022Article
- Role of Bifidobacterium pseudocatenulatum in Degradation and Consumption of Xylan-Derived Carbohydrates.Applied and environmental microbiology · 2022Article
- Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes.The ISME journal · 2022Article
- New perspectives on an old grouping: The genomic and phenotypic variability ofFrontiers in microbiology · 2022Article
- The Unique Seed Protein Composition of Quality Protein Popcorn Promotes Growth of Beneficial Bacteria From the Human Gut Microbiome.Frontiers in microbiology · 2022Article
- Captive Common Marmosets (Callithrix jacchus) Are Colonized throughout Their Lives by a Community ofmBio · 2021Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationDesigning PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico.
resultsHere we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers. AVAILABILITY AND IMPLEMENTATION: Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS. CONTACT: mcft@cbs.dtu.dk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.