PrimeSpecPCR: Python toolkit for species-specific DNA primer design and specificity testing

IF 2.4 4区计算机科学 Q2 COMPUTER SCIENCE, SOFTWARE ENGINEERING

SoftwareX Pub Date : 2025-06-28 DOI:10.1016/j.softx.2025.102249

Adam Kuzdraliński

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Abstract

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.

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primspecpcr：用于物种特异性DNA引物设计和特异性测试的Python工具包

primspecpcr是一个开源的Python工具包，可以自动化特定物种引物设计（包括正向引物、反向引物和探针）和验证的工作流程。该软件实现了模块化架构，主要包括四个部分：(1)基于分类标识符的NCBI数据库基因序列自动检索；(2)利用MAFFT进行多序列比对，生成一致性序列；(3)利用Primer3-py对引物和探针进行热动力学优化设计；(4)针对NCBI GenBank数据库进行多层特异性检测。该工具包具有用户友好的图形界面和可定制的定量PCR （qPCR）应用参数。primspecpcr通过并行处理、中间结果的自动缓存和生成交互式HTML报告来加速引物开发，这些报告可以可视化地显示跨分类组的特异性概况，同时最大限度地减少人为错误并确保结果的可重复性。该工具包减少了设计物种特异性分子分析通常需要的耗时、费力的过程。

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来源期刊

SoftwareX COMPUTER SCIENCE, SOFTWARE ENGINEERING-

CiteScore

5.50

自引率

2.90%

发文量

184

审稿时长

9 weeks

期刊介绍： SoftwareX aims to acknowledge the impact of software on today''s research practice, and on new scientific discoveries in almost all research domains. SoftwareX also aims to stress the importance of the software developers who are, in part, responsible for this impact. To this end, SoftwareX aims to support publication of research software in such a way that: The software is given a stamp of scientific relevance, and provided with a peer-reviewed recognition of scientific impact; The software developers are given the credits they deserve; The software is citable, allowing traditional metrics of scientific excellence to apply; The academic career paths of software developers are supported rather than hindered; The software is publicly available for inspection, validation, and re-use. Above all, SoftwareX aims to inform researchers about software applications, tools and libraries with a (proven) potential to impact the process of scientific discovery in various domains. The journal is multidisciplinary and accepts submissions from within and across subject domains such as those represented within the broad thematic areas below: Mathematical and Physical Sciences; Environmental Sciences; Medical and Biological Sciences; Humanities, Arts and Social Sciences. Originating from these broad thematic areas, the journal also welcomes submissions of software that works in cross cutting thematic areas, such as citizen science, cybersecurity, digital economy, energy, global resource stewardship, health and wellbeing, etcetera. SoftwareX specifically aims to accept submissions representing domain-independent software that may impact more than one research domain.