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Bioremediation Pathway Tool
Summary
Scientists have released a free software tool that scans bacterial DNA to identify which bacteria can break down pollutants, including plastics like PET (used in bottles), PU, PCL, and PBAT. This matters because microplastics are increasingly found in our water, food, and even human bodies, and this tool could help researchers find and harness plastic-eating bacteria for real-world cleanup solutions faster and more reliably. It's important to note this is a research tool for scientists rather than a ready-made cleanup solution, but it lays groundwork for future bioremediation efforts that could reduce plastic pollution and human exposure over time.
Bioremediation Pathway Tool v0.1.0 First public release of Bioremediation Pathway Tool, a pathway-level bioinformatics tool for conservative evidence-based detection of bioremediation-associated reactions and pathways from annotated bacterial genomes. Highlights Pathway-level analysis of annotated bacterial genomes in GenBank format. Curated core database containing 34 pathway/modules, 81 reactions, and 379 reference proteins. Conservative separation of supported, review, candidate, and not-detected evidence. Cross-reaction adjudication to reduce inflation of evidence from shared loci. Hybrid sequence-based rescue of unresolved annotations. Component-aware handling of multi-component reactions. Table-first HTML reporting with pathway completeness and evidence interpretation. Optional microplastics module covering curated PET, PCL, PBAT, and PU-associated reactions. GenBank input validation and normalization without modification of the original input genome. Release audit and regression tests included for reproducibility. Validation The v0.1.0 release passed the bundled release audit, including core database integrity, PET regression locking, PCL strict-gate testing, synthetic annotation positive controls, and checks for unintended local absolute paths. Citation Citation metadata is provided in CITATION.cff. This release is archived through Zenodo for persistent citation and DOI assignment. Authors Monira Mehzabin Khandoker Md Rezwan License Released under the MIT License.