AnoPrimer

AnoPrimer designs primers and probes for Anopheles malaria vectors by integrating range-wide genomic variation data to avoid amplification problems caused by single nucleotide polymorphisms (SNPs).

Key Features:

• Genomic variation integration: Exploits the Ag1000G and Af1000 datasets to summarize genetic variation in primer binding sites.
• Primer and probe design: Supports design of genomic DNA primers, cDNA primers, and hybridisation probes.
• Primer binding site visualization: Generates clear, interactive visualisations of primer pair positions and binding sites.
• Species coverage: Enables primer design across the Anopheles gambiae and Anopheles funestus species ranges.

Scientific Applications:

• PCR assay design: Designs reliable primers for polymerase chain reaction (PCR)-based molecular assays in highly genetically diverse malaria vectors.
• Hybridisation-based assay design: Designs probes for hybridisation-based molecular assays in An. gambiae and An. funestus.
• Null allele prevention: Avoids primer binding site mutations that prevent primer binding and cause null alleles.
• Allelic bias prevention: Avoids suboptimal primer binding to SNP variants that lead to preferential amplification of specific alleles.

Methodology:

AnoPrimer is implemented as a Python package that integrates whole-genome sequence data from the cloud and couples with Google Colaboratory for cloud-based execution.