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Updated: Aug 15, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
PRAWNS: compact pan-genomic features for whole-genome population genomics
Kiran Javkar1,2, Hugh Rand3, Errol Strain4
1Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
Motivation:
Scientists seeking to understand the genomic basis of bacterial phenotypes, such as antibiotic resistance, today have access to an unprecedented number of complete and nearly complete genomes. Making sense of these data requires computational tools able to perform multiple-genome comparisons efficiently, yet currently available tools cannot scale beyond several tens of genomes.
Results:
We describe PRAWNS, an efficient and scalable tool for multiple-genome analysis. PRAWNS defines a concise set of genomic features (metablocks), as well as pairwise relationships between them, which can be used as a basis for large-scale genotype-phenotype association studies. We demonstrate the effectiveness of PRAWNS by identifying genomic regions associated with antibiotic resistance in Acinetobacter baumannii.
Availability And Implementation:
PRAWNS is implemented in C++ and Python3, licensed under the GPLv3 license, and freely downloadable from GitHub (https://github.com/KiranJavkar/PRAWNS.git).
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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