PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing
PrimeSpecPCR is an open-source Python toolkit that automates the workflow of species-specific primer design (comprising forward primer, reverse primer, and probe) and validation. The software implements a modular architecture comprising four main components: (1) automated retrieval of genetic sequen...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-09-01
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| Series: | SoftwareX |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S235271102500216X |
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| author | Adam Kuzdraliński |
| author_facet | Adam Kuzdraliński |
| author_sort | Adam Kuzdraliński |
| collection | DOAJ |
| description | PrimeSpecPCR is an open-source Python toolkit that automates the workflow of species-specific primer design (comprising forward primer, reverse primer, and probe) and validation. The software implements a modular architecture comprising four main components: (1) automated retrieval of genetic sequences from NCBI databases based on taxonomy identifiers; (2) multiple sequence alignment using MAFFT to generate consensus sequences; (3) thermodynamically optimized primer and probe design via Primer3-py; and (4) multi-tiered specificity testing against the NCBI GenBank database. The toolkit features a user-friendly graphical interface and customizable parameters for quantitative PCR (qPCR) applications. PrimeSpecPCR accelerates primer development through parallel processing, automatic caching of intermediate results, and production of interactive HTML reports that visualize specificity profiles across taxonomic groups, while minimizing human errors and ensuring reproducibility of results. This toolkit reduces the time-intensive, labour-demanding processes conventionally required for designing species-specific molecular assays. |
| format | Article |
| id | doaj-art-96853c2f0a4c44b0b20a2bb7b1e35f49 |
| institution | Matheson Library |
| issn | 2352-7110 |
| language | English |
| publishDate | 2025-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SoftwareX |
| spelling | doaj-art-96853c2f0a4c44b0b20a2bb7b1e35f492025-06-30T04:09:01ZengElsevierSoftwareX2352-71102025-09-0131102249PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testingAdam Kuzdraliński0Department of Bioinformatics, Faculty of Information Technology, Polish-Japanese Academy of Information Technology, Warsaw, Mazowieckie 02-008, PolandPrimeSpecPCR is an open-source Python toolkit that automates the workflow of species-specific primer design (comprising forward primer, reverse primer, and probe) and validation. The software implements a modular architecture comprising four main components: (1) automated retrieval of genetic sequences from NCBI databases based on taxonomy identifiers; (2) multiple sequence alignment using MAFFT to generate consensus sequences; (3) thermodynamically optimized primer and probe design via Primer3-py; and (4) multi-tiered specificity testing against the NCBI GenBank database. The toolkit features a user-friendly graphical interface and customizable parameters for quantitative PCR (qPCR) applications. PrimeSpecPCR accelerates primer development through parallel processing, automatic caching of intermediate results, and production of interactive HTML reports that visualize specificity profiles across taxonomic groups, while minimizing human errors and ensuring reproducibility of results. This toolkit reduces the time-intensive, labour-demanding processes conventionally required for designing species-specific molecular assays.http://www.sciencedirect.com/science/article/pii/S235271102500216XPCR primersPCR primer designSpecies-specific primersBioinformatics |
| spellingShingle | Adam Kuzdraliński PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing SoftwareX PCR primers PCR primer design Species-specific primers Bioinformatics |
| title | PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing |
| title_full | PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing |
| title_fullStr | PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing |
| title_full_unstemmed | PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing |
| title_short | PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing |
| title_sort | primespecpcr python toolkit for species specific dna primer design and specificity testing |
| topic | PCR primers PCR primer design Species-specific primers Bioinformatics |
| url | http://www.sciencedirect.com/science/article/pii/S235271102500216X |
| work_keys_str_mv | AT adamkuzdralinski primespecpcrpythontoolkitforspeciesspecificdnaprimerdesignandspecificitytesting |