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Prokka: rapid prokaryotic genome annotation

https://doi.org/10.1093/bioinformatics/btu153
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nmeth.1701openalex-snapshot
SignalP 4.0: discriminating signal peptides from transmembrane regions
inferredcites →https://doi.org/10.1093/bib/bbs007openalex-snapshot
The automatic annotation of bacterial genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btp097openalex-snapshot
DIYA: a bacterial annotation pipeline for any genomics lab
inferredcites →https://doi.org/10.1093/bioinformatics/btr545openalex-snapshot
Fast filtering for RNA homology search
inferredcites →https://doi.org/10.1093/nar/30.1.276openalex-snapshot
The Pfam Protein Families Database
inferredcites →https://doi.org/10.1093/nar/gkh131openalex-snapshot
UniProt: the Universal Protein knowledgebase
inferredcites →https://doi.org/10.1093/nar/gkh152openalex-snapshot
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
inferredcites →https://doi.org/10.1093/nar/gkm160openalex-snapshot
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
inferredcites →https://doi.org/10.1093/nar/gkm928openalex-snapshot
xBASE2: a comprehensive resource for comparative bacterial genomics
inferredcites →https://doi.org/10.1093/nar/gkr1065openalex-snapshot
The Pfam protein families database
inferredcites →https://doi.org/10.1093/nar/gks1234openalex-snapshot
TIGRFAMs and Genome Properties in 2013
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot
Prodigal: prokaryotic gene recognition and translation initiation site identification
inferredcites →https://doi.org/10.1186/1471-2164-9-75openalex-snapshot
The RAST Server: Rapid Annotations using Subsystems Technology
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1002/lno.11243openalex-snapshot
Non‐cyanobacterial diazotrophs dominate nitrogen‐fixing communities in permafrost thaw ponds
inferred← citeshttps://doi.org/10.1002/lno.11361openalex-snapshot
The global Microcystis interactome
inferred← citeshttps://doi.org/10.1002/lno.11981openalex-snapshot
Oxygen‐deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments
inferred← citeshttps://doi.org/10.1002/lol2.10337openalex-snapshot
Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long‐read genome sequencing
inferred← citeshttps://doi.org/10.1002/mbo3.1019openalex-snapshot
Pantoea sp. P37 as a novel nonpathogenic host for the heterologous production of rhamnolipids
inferred← citeshttps://doi.org/10.1002/mbo3.1023openalex-snapshot
Isolation of an antimicrobial‐resistant, biofilm‐forming, Klebsiella grimontii isolate from a reusable water bottle
inferred← citeshttps://doi.org/10.1002/mbo3.1138openalex-snapshot
Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two‐component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies
inferred← citeshttps://doi.org/10.1002/mbo3.1175openalex-snapshot
Enrichment of novel Verrucomicrobia , Bacteroidetes , and Krumholzibacteria in an oxygen‐limited methane‐ and iron‐fed bioreactor inoculated with Bothnian Sea sediments
inferred← citeshttps://doi.org/10.1002/mbo3.1256openalex-snapshot
Transcriptomic analysis of Streptococcus agalactiae periprosthetic joint infection
inferred← citeshttps://doi.org/10.1002/mbo3.1298openalex-snapshot
Introduction to the principles and methods underlying the recovery of metagenome‐assembled genomes from metagenomic data
inferred← citeshttps://doi.org/10.1002/mbo3.1329openalex-snapshot
Brucella ceti and Brucella pinnipedialis genome characterization unveils genetic features that highlight their zoonotic potential
inferred← citeshttps://doi.org/10.1002/mbo3.1333openalex-snapshot
The emergence of the tetrathionate reductase operon in the Escherichia coli/Shigella pan‐genome
inferred← citeshttps://doi.org/10.1002/mbo3.1339openalex-snapshot
Bioinformatic survey of CRISPR loci across 15 Serratia species
inferred← citeshttps://doi.org/10.1002/mbo3.1348openalex-snapshot
The abundance of the potential pathogen Staphylococcus hominis in the air microbiome in a dental clinic and its susceptibility to far‐UVC light
inferred← citeshttps://doi.org/10.1002/mbo3.1352openalex-snapshot
Genomics of the “tumorigenes” clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.
inferred← citeshttps://doi.org/10.1002/mbo3.1389openalex-snapshot
Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity
inferred← citeshttps://doi.org/10.1002/mbo3.1394openalex-snapshot
Group A Streptococcus strains causing meningitis without distinct invasive phenotype
inferred← citeshttps://doi.org/10.1002/mbo3.1395openalex-snapshot
Serratia‐based toxin cluster elements are associated with a type I fimbria
inferred← citeshttps://doi.org/10.1002/mbo3.1396openalex-snapshot
Genomic analyses of an Escherichia coli and Klebsiella pneumoniae urinary tract co‐infection using long‐read nanopore sequencing
inferred← citeshttps://doi.org/10.1002/mbo3.1402openalex-snapshot
Complete nucleotide sequence and comparative genomic analysis of microcin B17 plasmid pMccB17
inferred← citeshttps://doi.org/10.1002/mbo3.1403openalex-snapshot
Genomic characterization of extended‐spectrum beta‐lactamase‐producing and carbapenem‐resistant Escherichia coli from urban wastewater in Australia
inferred← citeshttps://doi.org/10.1002/mbo3.1409openalex-snapshot
Multidrug‐resistant Stenotrophomonas maltophilia in residential aged care facilities: An emerging threat
inferred← citeshttps://doi.org/10.1002/mbo3.1431openalex-snapshot
Reassessment of the genetic basis of natural rifampin resistance in the genus Rickettsia
inferred← citeshttps://doi.org/10.1002/mbo3.1432openalex-snapshot
Extraction of high‐molecular‐weight DNA from Streptococcus spp. for nanopore sequencing in resource‐limited settings
inferred← citeshttps://doi.org/10.1002/mbo3.508openalex-snapshot
Alterations of c‐di‐ GMP turnover proteins modulate semi‐constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli
inferred← citeshttps://doi.org/10.1002/mbo3.70060openalex-snapshot
Profiling Listeria monocytogenes in Hummus, Fresh Produce, and Food Processing Environments in the Western Cape, South Africa
inferred← citeshttps://doi.org/10.1002/mbo3.70073openalex-snapshot
The Road Less Traveled: Exploring the Genomic Characteristics and Antimicrobial Resistance Potential of Acinetobacter baumannii From the Indigenous Orang Asli Community in Peninsular Malaysia
inferred← citeshttps://doi.org/10.1002/mbo3.70101openalex-snapshot
Phylogeny, Synteny, and Distribution of Type III Secretion Systems in Burkholderia cenocepacia : A Closer Look Into Host Span
inferred← citeshttps://doi.org/10.1002/mbo3.70131openalex-snapshot
Emergence of Livestock‐Associated Methicillin‐Resistant Staphylococcus aureus ST398 in Wild Birds, Brazil
inferred← citeshttps://doi.org/10.1002/mbo3.70133openalex-snapshot
“Expanding the Lactococcal Cell Wall Polysaccharide Paradigm: Novel Structures and Metabolic Pathways in the Emerging Dairy Species Pseudolactococcus laudensis and Pseudolactococcus raffinolactis ”
inferred← citeshttps://doi.org/10.1002/mbo3.70141openalex-snapshot
In House Rapid, Simple Multiple‐Locus Variable‐Number Tandem Repeat Analysis (MLVA): A Reliable Tool for Enterobacter hormaechei Genotyping
inferred← citeshttps://doi.org/10.1002/mbo3.70165openalex-snapshot
The Host R‐M Systems Change the Host Range of Staphylococcus Phage EBHT
inferred← citeshttps://doi.org/10.1002/mbo3.70176openalex-snapshot
Campylobacter Species Isolated From Wild Birds in Switzerland and Comparison to Isolates From Food and Human Origin
inferred← citeshttps://doi.org/10.1002/mbo3.70274openalex-snapshot
Whole‐Genome Sequence Profiling of Listeria innocua From Different Sources: Implications for Public Health
inferred← citeshttps://doi.org/10.1002/mbo3.70277openalex-snapshot
Of Commensals and Opportunists: Genomics of Coagulase‐Negative Staphylococci During Sequential Ear and Eye Infections in a Healthy Adult
inferred← citeshttps://doi.org/10.1002/mbo3.70314openalex-snapshot
Emerging Dissemination of bla CTX‐M‐65 in Bovine E. coli in Spain Associated With IncHI2 Plasmids
inferred← citeshttps://doi.org/10.1002/mbo3.70325openalex-snapshot
A Complete Genome Resource and Bio‐Control Activity of Soil‐Isolated Pseudomonas citronellolis Strain M03 Against Onion‐Pathogenic Burkholderia Species
inferred← citeshttps://doi.org/10.1002/mbo3.70344openalex-snapshot
Human Gut Phageome Analysis Uncovers Thousands of Highly Modular Endolysins
inferred← citeshttps://doi.org/10.1002/mbo3.70376openalex-snapshot
Experimental, Genomic, and Structural Evidence Supporting Putative PET‐Hydrolases in Thermophilic Bacteria Isolated From Hot Springs in Cajamarca, Peru
inferred← citeshttps://doi.org/10.1002/mbo3.70406openalex-snapshot
Comparative Genomic Analysis of Multidrug‐Resistant Escherichia coli Across Poultry–Human–Environmental Interfaces
inferred← citeshttps://doi.org/10.1002/mbo3.70425openalex-snapshot
First Report of bla CTX ‐ M‐15 in a Marine Thermotolerant Enterobacter Isolate From Bangladesh: Genomic Insights Into Halotolerance and Antimicrobial Resistance
inferred← citeshttps://doi.org/10.1002/mbo3.731openalex-snapshot
Comparative genomics of the Komagataeibacter strains—Efficient bionanocellulose producers
inferred← citeshttps://doi.org/10.1002/mbo3.754openalex-snapshot
Characteristics of crude oil‐degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment
inferred← citeshttps://doi.org/10.1002/mbo3.801openalex-snapshot
Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens
inferred← citeshttps://doi.org/10.1002/mbo3.842openalex-snapshot
Bioactivities and genome insights of a thermotolerant antibiotics‐producing Streptomyces sp. TM32 reveal its potentials for novel drug discovery
inferred← citeshttps://doi.org/10.1002/mbo3.844openalex-snapshot
lptG contributes to changes in membrane permeability and the emergence of multidrug hypersusceptibility in a cystic fibrosis isolate of Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.1002/mbo3.938openalex-snapshot
Insights into the genome structure of four acetogenic bacteria with specific reference to the Wood–Ljungdahl pathway
inferred← citeshttps://doi.org/10.1002/mbo3.972openalex-snapshot
Evolutionary changes of an intestinal Lactobacillus reuteri during probiotic manufacture
inferred← citeshttps://doi.org/10.1002/mco2.70569openalex-snapshot
Divergent Evolution and Local Establishment of Multidrug‐Resistant Shigella sonnei in China
inferred← citeshttps://doi.org/10.1002/mco2.70617openalex-snapshot
Genomic‐Based Epidemiological Analysis of the Post‐Pandemic Mycoplasma pneumoniae Resurgence
inferred← citeshttps://doi.org/10.1002/mco2.70814openalex-snapshot
Longitudinal Molecular Epidemiology and Genomic Surveillance of Carbapenem‐Resistant Klebsiella pneumoniae in the Gut of Healthy Individuals in China
inferred← citeshttps://doi.org/10.1002/mlf2.12041openalex-snapshot
Integrated identification of growth pattern and taxon of bacterium in gut microbiota via confocal fluorescence imaging‐oriented single‐cell sequencing
inferred← citeshttps://doi.org/10.1002/mlf2.12045openalex-snapshot
High‐efficiency genome editing of an extreme thermophile Thermus thermophilus using endogenous type I and type III CRISPR‐Cas systems
inferred← citeshttps://doi.org/10.1002/mlf2.70003openalex-snapshot
Leveraging collateral sensitivity to counteract the evolution of bacteriophage resistance in bacteria
inferred← citeshttps://doi.org/10.1002/mlf2.70029openalex-snapshot
The global genomic landscape of hypervirulent Klebsiella pneumoniae from 1932 to 2021
inferred← citeshttps://doi.org/10.1002/mlf2.70097openalex-snapshot
Thirteen‐year genomic analysis (2010–2022) reveals high‐risk ICU Pseudomonas aeruginosa in China
inferred← citeshttps://doi.org/10.1002/mlf2.70105openalex-snapshot
IS Aba1‐ mediated crp‐osmC amplification enhances host‐associated fitness in Acinetobacter baumannii
inferred← citeshttps://doi.org/10.1002/mnfr.202101098openalex-snapshot
Long‐Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis
inferred← citeshttps://doi.org/10.1002/mnfr.70209openalex-snapshot
Functional Genomics and Probiotic Traits of Lactiplantibacillus plantarum MB685 from Fermented Broccoli: Gut Health and Metabolic Insights
inferred← citeshttps://doi.org/10.1002/mnfr.70514openalex-snapshot
Bile Acid Deconjugation and Anti‐ Helicobacter pylori Activity of Limosilactobacillus reuteri DSM 34531
inferred← citeshttps://doi.org/10.1002/mnfr.70615openalex-snapshot
Metabolization of Flavan‐3‐ol Oligomers by Eggerthella lenta , a Human Gut Bacterium
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