SNPraefentia: a toolkit to prioritize microbial genome variants linked to health and disease
Year: 2024
Type: article
Abstract: Motivation: Analysis of genomic variation in microbial genomes is crucial for understanding how microbes adapt, interact with their hosts, and influence health and disease. In metagenomic studies, where genetic material from entire microbial communities is sequenced, thousands of single-nucleotide polymorphisms can be detected across species and samples. However, identifying which of these variations has biologically or functionally relevant impacts remains a significant challenge. Results: To address this, we present SNPraefentia, a Python-based toolkit for prioritizing microbial SNPs based on their predicted functional relevance. The tool integrates multiple biologically meaningful parameters, including sequencing depth, physicochemical impact of amino acid substitutions, and the structural and functional context of mutations within annotated protein domains. SNPraefentia extracts variation depth and amino acid changes, annotates protein domains using UniProt, and computes individual impact scores. These are then integrated into a composite prioritization score that reflects the potential biological importance of each variant. Overall, SNPraefentia provides researchers with a systematic and reproducible approach to filter and rank microbial variants for downstream functional analysis or experimental validation. Availability and implementation: The toolkit and test data are freely available at https://github.com/muneebdev7/SNPraefentia.
Source: Bioinformatics Advances
Authors: Nadeem Khan, Muhammad Muneeb Nasir, Ammar Mushtaq, Masood Ur Rehman Kayani
Institution: National University of Sciences and Technology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,917
OpenAlex ID: W4416821016