Nagi Sanjay C, Ashraf Faisal, Miles Alistair, Donnelly Martin J
Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK.
Wellcome Sanger Institute, Hinxton, England, UK.
Wellcome Open Res. 2024 May 15;9:255. doi: 10.12688/wellcomeopenres.20998.1. eCollection 2024.
The major malaria mosquitoes, and , are some of the most studied organisms in medical research and also some of the most genetically diverse. When designing polymerase chain reaction (PCR) or hybridisation-based molecular assays, reliable primer and probe design is crucial. However, single nucleotide polymorphisms (SNPs) in primer binding sites can prevent primer binding, leading to null alleles, or bind suboptimally, leading to preferential amplification of specific alleles. Given the extreme genetic diversity of mosquitoes, researchers need to consider this genetic variation when designing primers and probes to avoid amplification problems. In this note, we present a Python package, AnoPrimer, which exploits the Ag1000G and Af1000 datasets and allows users to rapidly design primers in or whilst summarising genetic variation in the primer binding sites and visualising the position of primer pairs. AnoPrimer allows the design of both genomic DNA and cDNA primers and hybridisation probes. By coupling this Python package with Google Colaboratory, AnoPrimer is an open and accessible platform for primer and probe design, hosted in the cloud for free. AnoPrimer is available here https://github.com/sanjaynagi/AnoPrimer and we hope it will be a useful resource for the community to design probe and primer sets that can be reliably deployed across the and species ranges.
主要的疟疾传播蚊子，即按蚊和冈比亚按蚊，是医学研究中研究最多的生物之一，也是遗传多样性最高的生物之一。在设计基于聚合酶链反应（PCR）或杂交的分子检测方法时，可靠的引物和探针设计至关重要。然而，引物结合位点中的单核苷酸多态性（SNP）可能会阻止引物结合，导致无效等位基因，或者结合效果不佳，导致特定等位基因的优先扩增。鉴于按蚊的极端遗传多样性，研究人员在设计引物和探针时需要考虑这种遗传变异，以避免扩增问题。在本说明中，我们展示了一个Python软件包AnoPrimer，它利用Ag1000G和Af1000数据集，允许用户在按蚊或冈比亚按蚊中快速设计引物，同时总结引物结合位点的遗传变异并可视化引物对的位置。AnoPrimer允许设计基因组DNA和cDNA引物以及杂交探针。通过将这个Python软件包与谷歌Colaboratory相结合，AnoPrimer是一个开放且易于使用的引物和探针设计平台，免费托管在云端。AnoPrimer可在此处获取：https://github.com/sanjaynagi/AnoPrimer，我们希望它将成为社区设计可在按蚊和冈比亚按蚊物种范围内可靠部署的探针和引物集的有用资源。
