ArticleGenes & genomics2025
In-silico matching of SARS-CoV-2 genes and oligonucleotides using the Simple Oligo Matching Tool.
Article in Genes & genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
1 citing paper in PubMed.
- A digital PCR-based platform for rapid assessment of chloroplast stress adaptation in microalgal metabolic engineering.Genes & genomics · 2026Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused a global pandemic, necessitating accurate diagnostic methods to control its spread. The World Health Organization (WHO) recommends nucleic acid amplification tests (NAATs), particularly reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR), as the diagnostic standard. Due to SARS-CoV-2’s high mutation rate, continuous validation of oligonucleotides (primers and probes) used in these tests is essential to ensure diagnostic accuracy.
objectiveCurrent validation tools for personal computers, such as Primer-BLAST, face limitations in handling large-scale genetic data and providing inclusivity analysis. To address these issues, we developed the Simple Oligo Matching Tool, a Python-based tool to facilitate in-silico analysis.
methodsThe performance of the Simple Oligo Matching Tool was assessed by comparing it with Primer-BLAST using a small-scale database, in which it demonstrated equivalent results. Additionally, this tool enables the analysis of oligonucleotide inclusivity and exclusivity across large-scale databases, identifying matches and mismatches with diverse SARS-CoV-2 variants and non-target microbes.
resultsThe Simple Oligo Matching Tool demonstrated equivalent performance to Primer-BLAST in small-scale analysis and further showed the capability to handle large-scale database analysis for both inclusivity and exclusivity. It successfully identified matches and mismatches with a wide variety of SARS-CoV-2 variants and non-target organisms.
conclusionThe Simple Oligo Matching Tool is expected to significantly reduce the complexity of large-scale in-silico analysis for non-commercial and commercial diagnostic development. It could be applied in various fields and could support continuous improvement and adaptation to respond to emerging infectious diseases.
Indexed as
Identifiers
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Registered trials
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