ArticleBMC bioinformatics2023
BADASS: BActeriocin-Diversity ASsessment Software.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 12 citations in OpenAlex.
- Leveraging strain competition to address antimicrobial resistance with microbiota therapies.Gut microbes · 2025Review
- Toward safer and sustainable food preservation: a comprehensive review of bacteriocins in the food industry.Bioscience reports · 2025Review
- Next generation sequencing as a panacea for antibiotic susceptibility testing: yea or nay?Frontiers in public health · 2025Article
- Bacteriocin diversity, function, discovery and application as antimicrobials.Nature reviews. Microbiology · 2024Review
- Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins.Microbial ecology · 2024Review
- Deep learning neural network development for the classification of bacteriocin sequences produced by lactic acid bacteria.F1000Research · 2024Article
- Immunomodulation, Bioavailability and Safety of Bacteriocins.Life (Basel, Switzerland) · 2023Review
- Modern Trends in Natural Antibiotic Discovery.Life (Basel, Switzerland) · 2023Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have a wide application including disease treatment, food conservation, and probiotics. However, even with a large industrial and biotechnological application potential, these peptides are still poorly studied and explored. BADASS is software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data.
resultsThe search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes of bacteriocins. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. BADASS has a complete pipeline that starts with the quality assessment of the raw data. At the end of the analysis, BADASS generates several plots of richness and abundance automatically as well as tabular files containing information about the main bacteriocins detected. The user is able to change the main parameters of the analysis in the graphical interface. To demonstrate how the software works, we used four datasets from WMS studies using default parameters. Lantibiotics were the most abundant bacteriocins in the four datasets. This class of bacteriocin is commonly produced by Streptomyces sp.
conclusionsWith a user-friendly graphical interface and a complete pipeline, BADASS proved to be a powerful tool for prospecting bacteriocin sequences in Whole-Metagenome Shotgun Sequencing (WMS) data. This tool is publicly available at https://sourceforge.net/projects/badass/ .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.