ArticleBioinformatics (Oxford, England)2014
Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG.
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Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25citing papers in PubMed
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Who cites it
25 citing papers in PubMed.
- Functional dynamics of the gut microbiome in elderly people during probiotic consumption.mBio · 2015Trial
- Comparative Genomic and Transcriptomic Analysis Reveals Why Paenarthrobacter Strains Are Specialists in the Degradation of the Fungicide Iprodione.Microbial biotechnology · 2026Article
- Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.Antimicrobial agents and chemotherapy · 2025Review
- Human iPS cell-derived respiratory organoids as a model for respiratory syncytial virus infection.Life science alliance · 2025Article
- Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs.Scientific reports · 2023Article
- Complete Genome Sequence of Pseudomonas sp. Strain 273, a Haloalkane-Degrading Bacterium.Microbiology resource announcements · 2023Article
- shinyCircos-V2.0: Leveraging the creation of Circos plot with enhanced usability and advanced features.iMeta · 2023Article
- GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.PLoS computational biology · 2023Article
- Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease.Microbiology spectrum · 2023Article
- Article
- Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut.Viruses · 2021Article
- Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems.Nature communications · 2020Article
- NG-Circos: next-generation Circos for data visualization and interpretation.NAR genomics and bioinformatics · 2020Article
- PACVr: plastome assembly coverage visualization in R.BMC bioinformatics · 2020Article
- Visualizing and comparing circular genomes using the CGView family of tools.Briefings in bioinformatics · 2019Review
- Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era.Current genomics · 2019Review
- Vesicles FromFrontiers in microbiology · 2019Article
- Characterization of LE3 and LE4, the only lytic phages known to infect the spirochete Leptospira.Scientific reports · 2018Article
- Complete Genome Sequence ofGenome announcements · 2017Article
- Characterization of a Large Antibiotic Resistance Plasmid Found in Enteropathogenic Escherichia coli Strain B171 and Its Relatedness to Plasmids of Diverse E. coli and Shigella Strains.Antimicrobial agents and chemotherapy · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Jonathan CrabtreeInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Sonia AgrawalInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Anup MahurkarInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Garry S MyersInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine
David A RaskoInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Owen WhiteInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, i3 Institute, University of Technology, Sydney, PO Box 123 Broadway NSW 2007, Australia, Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD 21201, Center for Health-Related Informatics and Bioimaging, University of Maryland, College Park, MD 20740 and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Funding
Technology CoreU19AI110820 · NIAID · UNIVERSITY OF MARYLAND BALTIMORE · PI DUNNING HOTOPP, JULIE · 2014 to 2023
$36.5MNIAID NIH HHS HHSN272200900009CNIAID NIH HHS U19 AI110820NIAID NIH HHS U19AI110820
Abstract
summaryCircleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It includes a library of circular track types and predefined configuration files for common use-cases, including. (i) visualizing gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene conservation in related microbial strains, (iii) showing Single Nucleotide Polymorphisms (SNPs) and indels relative to a reference genome and gene set and (iv) viewing RNA-Seq plots. AVAILABILITY AND IMPLEMENTATION: Circleator is freely available under the Artistic License 2.0 from http://jonathancrabtree.github.io/Circleator/ and is integrated with the CloVR cloud-based sequence analysis Virtual Machine (VM), which can be downloaded from http://clovr.org or run on Amazon EC2.
Indexed as
SoftwareComputer GraphicsGardnerella vaginalisGenomicsMolecular Sequence AnnotationPolymorphism, Single NucleotideSequence Analysis, DNASequence Analysis, RNA
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LicenceCC BY-NC
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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.