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AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation.

Nagi, Sanjay, Ashraf, Faisal, Miles, Alistair and Donnelly, Martin ORCID: https://orcid.org/0000-0001-5218-1497 (2024) 'AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation.'. Wellcome Open Research, Vol 9, e255.

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Abstract

The major malaria mosquitoes, Anopheles gambiae s.l and Anopheles funestus, 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 Anopheles 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 An. gambiae or An. funestus, 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 An. gambiae and funestus species ranges.

Item Type: Article
Subjects: QU Biochemistry > Genetics > QU 460 Genomics. Proteomics
WC Communicable Diseases > Tropical and Parasitic Diseases > WC 750 Malaria
Faculty: Department: Biological Sciences > Vector Biology Department
Digital Object Identifer (DOI): https://doi.org/10.12688/wellcomeopenres.20998.1
SWORD Depositor: JISC Pubrouter
Depositing User: JISC Pubrouter
Date Deposited: 23 Sep 2024 12:59
Last Modified: 23 Sep 2024 12:59
URI: https://archive.lstmed.ac.uk/id/eprint/25272

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