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Innovative Medicines & Omics Open source bioinformatics tools in Africa

3.4.4. Population linkage or pedigree linkage research to align sequences of drought-resistant crops, such

In addition to FastQC and BWA, tools like PLINK have as maize and sorghum. For example, in Kenya, researchers
been instrumental in analyzing large-scale genomic used MAFFT to compare the genomes of drought-tolerant
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datasets, enabling researchers to identify genetic variants and drought-susceptible maize varieties. This led to the
associated with complex diseases. It is a widely used open- identification of key genes (e.g., ZmDREB2A) involved
source toolset for genome-wide association studies and in drought resistance, the development of improved
genetic data analysis. For example, PLINK has been used crop varieties through marker-assisted breeding, and the
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in studies on HIV resistance in South Africa, providing enhancement of food security in drought-prone regions.
insights into host-pathogen interactions. In addition, MAFFT has been used to study genetic
diseases prevalent in Africa, such as sickle cell anemia.
3.4.5. Multiple alignment using fast Fourier transform By aligning sequences of the HBB gene from different
(MAFFT) populations, researchers have identified novel single
MAFFT is an open-source bioinformatics tool used nucleotide polymorphisms associated with disease severity
for multiple sequence alignment, which is essential and population-specific genetic markers for personalized
for comparing and analyzing DNA, RNA, or protein medicine.
sequences. MAFFT is known for its speed, accuracy, Besides infectious disease research and genomic
and ability to handle large datasets, making it a popular studies, MAFFT has also been used in phylogenetic
choice for phylogenetic analysis, evolutionary studies, and analysis. MAFFT has been used to construct phylogenetic
functional annotation.
trees for pathogens like M. tuberculosis (the causative agent
Key features of MAFFT include high accuracy, as it uses of TB) and SARS-CoV-2 (responsible for COVID-19). For
advanced algorithms (e.g., fast Fourier transform) to align example, during the COVID-19 pandemic, researchers
sequences with high precision, high speed (optimized for in South Africa used MAFFT to align viral genomes and
rapid alignment of large datasets, even with thousands track the emergence of the Beta variant (B.1.351). This
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of sequences), and flexibility, as it supports various enabled early detection of the variant, rapid public health
alignment strategies, including progressive, iterative, responses, including lockdowns and vaccine deployment,
and consistency-based methods. It is also user-friendly, and global sharing of genomic data through platforms like
offering both command-line and web-based interfaces GISAID.
for ease of use. It is compatible with other bioinformatics
tools for downstream analysis, such as phylogenetic tree In summary, these tools have fostered local expertise
construction. MAFFT has been instrumental in advancing in computational drug discovery, empowering African
researchers to develop homegrown solutions to regional
genomic and infectious disease research in Africa.
health problems.
Under HIV and Ebola research, MAFFT has been
used to align viral genomes from the HIV and Ebola 3.5. Structural biology insights: PDB
outbreaks in Africa. For example, during the 2014 – 2016 3.5.1. African contributions to structural biology
Ebola outbreak in West Africa, researchers used MAFFT
to align viral sequences from different patients. This African researchers have made significant contributions
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allowed them to track the evolution of the virus, identify on the global scientific stage. A notable example is the
key mutations associated with increased transmissibility deposition of the P. falciparum dihydrofolate reductase
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or virulence, and inform public health strategies, such as (PfDHFR) structure into the PDB. Molefe et al. showed
targeted containment and vaccine development. that inhibitors binding to PfDHFR could significantly
reduce its activity, which is critical for next-gen antimalarial
Moreover, MAFFT has been used to align sequences drugs. This demonstrates the region’s growing scientific
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of the P. falciparum parasite, which causes malaria. By prowess.
comparing sequences from different regions of Africa,
researchers have identified genetic variations linked to 3.5.2. PDB data for African-specific diseases
drug resistance. This has helped develop region-specific The PDB, combined with tools such asBioPython and
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treatment protocols and prevent the spread of drug- PyMOL, has transformed our understanding of pathogen
resistant malaria strains. structures. Structural analyses of the M. tuberculosis
For genomic studies, MAFFT has been employed in KasA protein revealed novel binding sites for potential
various fields, such as crop and human genomics. In the inhibitors. This work goes beyond academic curiosity; it
context of crop genomics, MAFFT was used in agricultural is vital for developing treatments tailored to Africa’s needs.

Volume 2 Issue 2 (2025) 57 doi: 10.36922/imo.8111