ArticleBMC bioinformatics2010
A high-throughput pipeline for the design of real-time PCR signatures.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets.BMC bioinformatics · 2025Article
- AutoPVPrimer: A comprehensive AI-Enhanced pipeline for efficient plant virus primer design and assessment.PloS one · 2025Article
- PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.mSphere · 2024Article
- Multicenter Preparedness Exercise Enables Rapid Development of Cluster-Specific PCR-Based Screening Assays from Bacterial Genomic Data.Journal of clinical 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
- Designing sensitive viral diagnostics with machine learning.Nature biotechnology · 2022Article
- End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection.Scientific reports · 2022Article
- Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary RegulatedMicroorganisms · 2021Review
- Article
- Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.Nucleic acids research · 2017Article
- HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing.Evolutionary bioinformatics online · 2016Article
- An algorithm of discovering signatures from DNA databases on a computer cluster.BMC bioinformatics · 2014Article
- PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.Nucleic acids research · 2014Article
- Repertoire of novel sequence signatures for the detection of Candidatus Liberibacter asiaticus by quantitative real-time PCR.BMC microbiology · 2014Article
- Primer3--new capabilities and interfaces.Nucleic acids research · 2012Article
- Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities.Journal of bioterrorism & biodefense · 2012Article
- Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains.PloS one · 2012Article
- SNIT: SNP identification for strain typing.Source code for biology and medicine · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPathogen diagnostic assays based on polymerase chain reaction (PCR) technology provide high sensitivity and specificity. However, the design of these diagnostic assays is computationally intensive, requiring high-throughput methods to identify unique PCR signatures in the presence of an ever increasing availability of sequenced genomes.
resultsWe present the Tool for PCR Signature Identification (TOPSI), a high-performance computing pipeline for the design of PCR-based pathogen diagnostic assays. The TOPSI pipeline efficiently designs PCR signatures common to multiple bacterial genomes by obtaining the shared regions through pairwise alignments between the input genomes. TOPSI successfully designed PCR signatures common to 18 Staphylococcus aureus genomes in less than 14 hours using 98 cores on a high-performance computing system.
conclusionsTOPSI is a computationally efficient, fully integrated tool for high-throughput design of PCR signatures common to multiple bacterial genomes. TOPSI is freely available for download at http://www.bhsai.org/downloads/topsi.tar.gz.
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