Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG

Jonathan Crabtree; Sonia Agrawal; Anup Mahurkar; Garry S Myers; David A Rasko; Owen White

doi:10.1093/bioinformatics/btu505

Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG

Bioinformatics. 2014 Nov 1;30(21):3125-7. doi: 10.1093/bioinformatics/btu505. Epub 2014 Jul 29.

Authors

Jonathan Crabtree¹, Sonia Agrawal¹, Anup Mahurkar¹, Garry S Myers², David A Rasko³, Owen White³

Affiliations

¹ 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.
² 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, 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
³ 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, 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.

Abstract

Summary: Circleator 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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Computer Graphics
Gardnerella vaginalis / genetics
Genomics / methods*
Molecular Sequence Annotation
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Sequence Analysis, RNA
Software*

Abstract

Publication types

MeSH terms

Grants and funding