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

Crabtree, J; Agrawal, S; Mahurkar, A; Myers, GS; Rasko, DA; White, O

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

Crabtree, J Agrawal, S Mahurkar, A Myers, GS

Rasko, DA White, O

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Publication Type:: Journal Article
Citation:: Bioinformatics, 2014, 30 (21), pp. 3125 - 3127
Issue Date:: 2014-01-01

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Field	Value	Language
dc.contributor.author	Crabtree, J	en_US
dc.contributor.author	Agrawal, S	en_US
dc.contributor.author	Mahurkar, A	en_US
dc.contributor.author	Myers, GS https://orcid.org/0000-0002-4756-4810	en_US
dc.contributor.author	Rasko, DA	en_US
dc.contributor.author	White, O	en_US
dc.date.issued	2014-01-01	en_US
dc.identifier.citation	Bioinformatics, 2014, 30 (21), pp. 3125 - 3127	en_US
dc.identifier.issn	1367-4803	en_US
dc.identifier.uri	http://hdl.handle.net/10453/33898
dc.description.abstract	© The Author 2014. Published by Oxford University Press. 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.	en_US
dc.relation.ispartof	Bioinformatics	en_US
dc.relation.isbasedon	10.1093/bioinformatics/btu505	en_US
dc.subject.classification	Bioinformatics	en_US
dc.subject.mesh	Gardnerella vaginalis	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Sequence Analysis, RNA	en_US
dc.subject.mesh	Genomics	en_US
dc.subject.mesh	Polymorphism, Single Nucleotide	en_US
dc.subject.mesh	Computer Graphics	en_US
dc.subject.mesh	Software	en_US
dc.subject.mesh	Molecular Sequence Annotation	en_US
dc.title	Circleator: Flexible circular visualization of genome-associated data with BioPerl and SVG	en_US
dc.type	Journal Article
utslib.citation.volume	21	en_US
utslib.citation.volume	30	en_US
utslib.for	060102 Bioinformatics	en_US
utslib.for	01 Mathematical Sciences	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	08 Information and Computing Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
utslib.copyright.status	closed_access
pubs.issue	21	en_US
pubs.publication-status	Published	en_US
pubs.volume	30	en_US

Abstract:

© The Author 2014. Published by Oxford University Press. 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.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/33898