publication . Article . 2016

PanViz: interactive visualization of the structure of functionally annotated pangenomes.

Thomas Lin Pedersen;
Open Access English
  • Published: 01 Dec 2016
  • Country: Denmark
Abstract
Abstract Summary: PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses. Availability and Implementation: PanViz is written entirely in JavaScript and is available on https:/...
Subjects
free text keywords: Applications Notes, Genome Analysis
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Ashburner M.et al (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25–29.10802651 [OpenAIRE] [PubMed]

Bostock M.et al (2011) D 3: Data-Driven Documents. IEEE Trans. Vis. Comput. Graph., 17, 2301–2309.22034350 [OpenAIRE] [PubMed]

Cain A.A.et al (2012) GenoSets: visual analytic methods for comparative genomics. PLoS ONE, 7, e46401.23056299 [OpenAIRE] [PubMed]

Conesa A.et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674–3676.16081474 [OpenAIRE] [PubMed]

Gentleman R.C.et al (2003) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80–R80.

Grant J.R.et al (2012) Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics, 13, 202.22621371 [OpenAIRE] [PubMed]

Hallin P.F.et al (2008) The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol. bioSyst., 4, 363–371.18414733 [OpenAIRE] [PubMed]

Herbig A.et al (2012) GenomeRing: alignment visualization based on SuperGenome coordinates. Bioinformatics, 28, i7–15.22689781 [OpenAIRE] [PubMed]

Huber W.et al (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods, 12, 115–121.25633503 [OpenAIRE] [PubMed]

Jones P.et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, 1236–1240.24451626 [OpenAIRE] [PubMed]

Land M.et al (2015) Insights from 20 years of bacterial genome sequencing. Funct. Integr. Genomics, 15, 141–161.25722247 [OpenAIRE] [PubMed]

Lechat P.et al (2012) SynTView – an interactive multi-view genome browser for next-generation comparative microorganism genomics. BMC Bioinformatics, 14, 277–277.

Rokicki J.et al (2014) CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. BMC Genomics, 15, 65.24460813 [OpenAIRE] [PubMed]

Zdobnov E.M., Apweiler R. (2001) InterProScan – an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847–848.11590104 [OpenAIRE] [PubMed]

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Abstract
Abstract Summary: PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses. Availability and Implementation: PanViz is written entirely in JavaScript and is available on https:/...
Subjects
free text keywords: Applications Notes, Genome Analysis
Related Organizations

Ashburner M.et al (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25–29.10802651 [OpenAIRE] [PubMed]

Bostock M.et al (2011) D 3: Data-Driven Documents. IEEE Trans. Vis. Comput. Graph., 17, 2301–2309.22034350 [OpenAIRE] [PubMed]

Cain A.A.et al (2012) GenoSets: visual analytic methods for comparative genomics. PLoS ONE, 7, e46401.23056299 [OpenAIRE] [PubMed]

Conesa A.et al (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674–3676.16081474 [OpenAIRE] [PubMed]

Gentleman R.C.et al (2003) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80–R80.

Grant J.R.et al (2012) Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics, 13, 202.22621371 [OpenAIRE] [PubMed]

Hallin P.F.et al (2008) The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol. bioSyst., 4, 363–371.18414733 [OpenAIRE] [PubMed]

Herbig A.et al (2012) GenomeRing: alignment visualization based on SuperGenome coordinates. Bioinformatics, 28, i7–15.22689781 [OpenAIRE] [PubMed]

Huber W.et al (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods, 12, 115–121.25633503 [OpenAIRE] [PubMed]

Jones P.et al (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30, 1236–1240.24451626 [OpenAIRE] [PubMed]

Land M.et al (2015) Insights from 20 years of bacterial genome sequencing. Funct. Integr. Genomics, 15, 141–161.25722247 [OpenAIRE] [PubMed]

Lechat P.et al (2012) SynTView – an interactive multi-view genome browser for next-generation comparative microorganism genomics. BMC Bioinformatics, 14, 277–277.

Rokicki J.et al (2014) CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. BMC Genomics, 15, 65.24460813 [OpenAIRE] [PubMed]

Zdobnov E.M., Apweiler R. (2001) InterProScan – an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847–848.11590104 [OpenAIRE] [PubMed]

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