ArticleFrontiers in genetics2022
DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation.
Article in Frontiers in genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 29 citations in OpenAlex.
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- Whole genome sequence-based comparative genomics reveals preliminary genomic features of Salmonella enterica subsp. enterica serovar Enteritidis phage type 1 and phage type 4 strains from EnteroBase.BMC microbiology · 2026Article
- Genomic Insight into the Mobility of Antibiotic Resistance Genes in Multidrug-ResistantAntibiotics (Basel, Switzerland) · 2026Article
- PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis.Nucleic acids research · 2026Article
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- Characterizing the ecological niche of insertion sequences within prokaryotic genomes.The ISME journal · 2026Article
- Prophage Activation: An In Silico Platform for Identifying Prophage Regulatory Elements to Inform Phage Engineering Against Drug-Resistant Bacteria.Life (Basel, Switzerland) · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota.Microbial ecology · 2025Article
- Molecular epidemiological study of Pseudomonas aeruginosa strains isolated from hospitals in Brazil by MLST and CRISPR/Cas system analysis.Molecular genetics and genomics : MGG · 2025Article
- Global epidemiology and resistance-related mutations of ceftazidime-avibactam-resistantFrontiers in cellular and infection microbiology · 2025Article
- Genomic analysis of carbapenem-resistantFrontiers in microbiology · 2025Article
- Genomic analysis of community-associated methicillin-resistantFrontiers in microbiology · 2025Article
- Whole-Genome Sequencing ofMicroorganisms · 2024Article
- Article
- VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes.NAR genomics and bioinformatics · 2024Article
- Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models.Microorganisms · 2024Article
- First Report of Carbapenem-ResistantInfection and drug resistance · 2024Article
- VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes.bioRxiv : the preprint server for biology · 2023Article
- CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As an intracellular form of a bacteriophage in the bacterial host genome, a prophage usually integrates into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). With the exponentially increasing number of microbial sequences uncovered in genomic or metagenomics studies, there is a massive demand for a tool that is capable of fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes. DBSCAN-SWA runs faster than any previous tools. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%), and PHASTER (82%) for (Multi-) FASTA sequences. Moreover, DBSCAN-SWA outperforms the existing standalone prophage prediction tools for high-throughput sequencing data based on the analysis of 19,989 contigs of 400 bacterial genomes collected from Human Microbiome Project (HMP) project. DBSCAN-SWA also provides user-friendly result visualizations including a circular prophage viewer and interactive DataTables. DBSCAN-SWA is implemented in Python3 and is available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.
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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.