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

doi:10.1093/bioinformatics/btu505

. 2014 Nov 1;30(21):3125-7.

doi: 10.1093/bioinformatics/btu505. Epub 2014 Jul 29.

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

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.

PMID: 25075113
PMCID: PMC4201160
DOI: 10.1093/bioinformatics/btu505

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

Jonathan Crabtree et al. Bioinformatics. 2014.

. 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.

PMID: 25075113
PMCID: PMC4201160
DOI: 10.1093/bioinformatics/btu505

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.

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Figures

**Fig. 1.**
(A) The genome of *Gardnerella vaginalis* HMP9231 annotated with percent GC content (red), genes, GC-skew (green) and read coverage (blue) from five human metagenomic samples. (B) SNPs from an 80-genome *Yersinia pestis* SNP panel with the scale in the outer rings expanded to show the affected bases. The reference base and position is shown on the outside and SNPS are color-coded according to their predicted type. Additional details for these figures and others may be found in the supplementary information

See this image and copyright information in PMC

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References

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1. Angiuoli S, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011;12:356. - PMC - PubMed
1. Arakawa K, et al. A Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics. 2009;10:31. - PMC - PubMed
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1. Bostock M, et al. D3: Data-driven documents. IEEE Trans. Vis. Comput. Graph. 2011;17:2301–2309. - PubMed

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[1] Alikhan NF, et al. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. - PMC - PubMed

[2] Alikhan NF, et al. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. - PMC - PubMed

[3] Angiuoli S, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011;12:356. - PMC - PubMed

[4] Angiuoli S, et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics. 2011;12:356. - PMC - PubMed

[5] Arakawa K, et al. A Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics. 2009;10:31. - PMC - PubMed

[6] Arakawa K, et al. A Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics. 2009;10:31. - PMC - PubMed

[7] Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–580. - PMC - PubMed

[8] Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–580. - PMC - PubMed

[9] Bostock M, et al. D3: Data-driven documents. IEEE Trans. Vis. Comput. Graph. 2011;17:2301–2309. - PubMed

[10] Bostock M, et al. D3: Data-driven documents. IEEE Trans. Vis. Comput. Graph. 2011;17:2301–2309. - PubMed

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

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

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