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GenomeVx: simple web-based creation of editable circular chromosome maps

GenomeVx: simple web-based creation of editable circular chromosome maps Vol. 24 no. 6 2008, pages 861–862 BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm598 Genome analysis GenomeVx: simple web-based creation of editable circular chromosome maps Gavin C. Conant and Kenneth H. Wolfe Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland Received on October 17, 2007; revised on November 21, 2007; accepted on November 28, 2007 Advance Access publication January 28, 2008 Associate Editor: Martin Bishop ABSTRACT mentioned above are very feature-rich. However, as a result, all must be installed locally by the user, and all also have some We describe GenomeVx, a web-based tool for making editable, combination of local library dependence, complex input publication-quality, maps of mitochondrial and chloroplast genomes formatting and output formats that are difficult to edit. We and of large plasmids. These maps show the location of genes and set out to create a simple Web-based tool (GenomeVx) for chromosomal features as well as a position scale. The program making circular maps. This program would not attempt to takes as input either raw feature positions or GenBank records. duplicate the features available with existing tools; rather it In the latter case, features are automatically extracted and colored, would aim to be as simple-to-use as possible, with a web-based an example of which is given. Output is in the Adobe Portable interface and an output format which would be accessible on Document Format (PDF) and can be edited by programs such as almost all hardware platforms. Adobe Illustrator. Our initial Postscript maps are generated by a Cþþ program Availability: GenomeVx is available at http://wolfe.gen.tcd.ie/ linked to the GNU plotutils package (http://www.gnu.org/ GenomeVx software/plotutils/). This program is wrapped into a CGI front- Contact: conantg@tcd.ie end (http://wolfe.gen.tcd.ie/GenomeVx) which allows users to input data either as a list of features and coordinates or as a Since the invention of Sanger sequencing (Sanger et al., 1977), preexisting GenBank flatfile. Because the Postscript format is the cost of DNA sequencing has fallen continually, and the not universally supported, GenomeVx’s output is an Adobe volume of sequence data in public databases has correspond- Portable Document Format file. Although the output from ingly risen (Collins et al., 2003). Thus, we estimate that the GenomeVx can be used directly for presentation (Fig. 1), we number of sequenced organellar genomes from eukaryotes has expect that most users will edit the resulting map with a doubled roughly every two years since the first such sequences program such as Adobe Illustrator. were published (data not shown; Ohyama et al., 1986; Figure 1 illustrates the unedited output from GenomeVx, Shinozaki et al., 1986). Indeed, the number of sequenced using the chloroplast genome sequence of the American angiosperm chloroplast genomes in GenBank tripled from 24 sycamore Platanus occidentalis (Moore et al., 2006) as input. at the end of 2005 to at least 73 at the end of 2007, and new The image shown was created directly from the features in the sequencing technologies are already pushing this number GenBank record for this genome (NC_008335). GenomeVx upward (Moore et al., 2006). does not attempt to correct for the occasional overlaps in One of us (KHW) sequenced one chloroplast genome in 1992 gene names shown, but the labels can be moved manually by and another in 2007. We were surprised to find that, although editing the PDF file. The colors in the Figure were produced the annotation toolkits for organelle genomes had improved automatically: genes are colored based on the first two letters of over this period (Wyman et al., 2004), there were still no easy- the gene name (except for ribosomal RNAs which are all given to-use, free web tools for making publication-quality genomic a single color). maps. Most papers reporting sequences of chloroplast or Input into GenomeVx can either be done manually by mitochondrial genomes include a circular map showing gene pasting genes or nucleotide features (e.g. SNPs) from a locations (Cai et al., 2006; Guo et al., 2007; Saski et al., 2005; program such as Microsoft Excel or by uploading a Talla et al., 2005). However, by making enquiries, we GenBank-format flatfile. When imported from a GenBank discovered that these maps are still often laboriously hand- file, coordinates appear as an editable list in the web interface, drawn, although there are at least three packages which can giving the user the option of overriding the automatic coloring generate them (Gibson and Smith, 2003; Sato and Ehira, 2003; decisions or editing the annotation. The program can also Stothard and Wishart, 2005). With all bioinformatics software there are trade-offs between include miscellaneous features on one or more inner scale rings ease-of-use and the number of features. The three tools (e.g. the inverted repeats in Fig. 1). GenomeVx is intended to simplify the study of organelle genomes by allowing biologists to produce circular genome *To whom correspondence should be addressed. maps without resorting to ad-hoc solutions. The web-based The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org 861 G.C.Conant and K.H.Wolfe Fig. 1. A chloroplast genome map produced by GenomeVx. Genes are colored in groups based on the first two letters of the gene name. A user- specified number of evenly spaced scale indices are produced after rounding the genome size to the nearest two digits (thus, the distance between the last label and 0 kb may be greater than between the other markers). GenomeVx can orient the map either anticlockwise from 3 O’clock (the convention for chloroplast genomes) or clockwise from 12 O’clock (the convention for mitochondrial genomes). Gibson,R. and Smith,D.R. (2003) Genome visualization made fast and simple. interface allows quick access without the installation of local Bioinformatics, 19, 1449–1450. software. We hope that GenomeVx will enable researchers who Guo,X. et al. (2007) Rapid evolutionary change of common bean (Phaseolus study circular genomes to spend less time drawing and more vulgaris L) plastome, and the genomic diversification of legume chloroplasts. time on topics of greater scientific interest. BMC Genomics, 8, 228. Moore,M.J. et al. (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol., 6, 17. Ohyama,K. et al. (1986) Chloroplast gene organization deduced from complete ACKNOWLEDGEMENTS sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature, 322, We thank K. Diekmann, A.C. Frank and J. Mower for 572–574. Sanger,F. et al. (1977) Nucleotide sequence of bacteriophage phi X174 DNA. suggestions during the design and testing of GenomeVx. Nature, 265, 687–695. We also thank K. Byrne and K. Hokamp for technical Saski,C. et al. (2005) Complete chloroplast genome sequence of Gycine max and assistance developing the web interface. This work was comparative analyses with other legume genomes. Plant Mol. Biol., 59, supported by Science Foundation Ireland. 309–322. Sato,N. and Ehira,S. (2003) GenoMap, a circular genome data viewer. Conflict of Interest: none declared. Bioinformatics, 19, 1583–1584. Shinozaki,K. et al. (1986) The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression. EMBO J., 5, 2043–2049. REFERENCES Stothard,P. and Wishart,D.S. (2005) Circular genome visualization and explora- tion using CGView. Bioinformatics, 21, 537–539. Cai,Z. et al. (2006) Complete plastid genome sequences of Drimys, Liriodendron, Talla,E. et al. (2005) The complete mitochondrial genome of the yeast and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol. Biol., 6,77. Kluyveromyces thermotolerans. FEBS Lett., 579, 30–40. Collins,F.S. et al. (2003) The human genome project: lessons from large-scale Wyman,S.K. et al. (2004) Automatic annotation of organellar genomes with biology. Science, 300, 286–290. DOGMA. Bioinformatics, 20, 3252–3255. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

GenomeVx: simple web-based creation of editable circular chromosome maps

Bioinformatics , Volume 24 (6): 2 – Jan 28, 2008

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Oxford University Press
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
ISSN
1367-4803
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1460-2059
DOI
10.1093/bioinformatics/btm598
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18227121
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Abstract

Vol. 24 no. 6 2008, pages 861–862 BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm598 Genome analysis GenomeVx: simple web-based creation of editable circular chromosome maps Gavin C. Conant and Kenneth H. Wolfe Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin 2, Ireland Received on October 17, 2007; revised on November 21, 2007; accepted on November 28, 2007 Advance Access publication January 28, 2008 Associate Editor: Martin Bishop ABSTRACT mentioned above are very feature-rich. However, as a result, all must be installed locally by the user, and all also have some We describe GenomeVx, a web-based tool for making editable, combination of local library dependence, complex input publication-quality, maps of mitochondrial and chloroplast genomes formatting and output formats that are difficult to edit. We and of large plasmids. These maps show the location of genes and set out to create a simple Web-based tool (GenomeVx) for chromosomal features as well as a position scale. The program making circular maps. This program would not attempt to takes as input either raw feature positions or GenBank records. duplicate the features available with existing tools; rather it In the latter case, features are automatically extracted and colored, would aim to be as simple-to-use as possible, with a web-based an example of which is given. Output is in the Adobe Portable interface and an output format which would be accessible on Document Format (PDF) and can be edited by programs such as almost all hardware platforms. Adobe Illustrator. Our initial Postscript maps are generated by a Cþþ program Availability: GenomeVx is available at http://wolfe.gen.tcd.ie/ linked to the GNU plotutils package (http://www.gnu.org/ GenomeVx software/plotutils/). This program is wrapped into a CGI front- Contact: conantg@tcd.ie end (http://wolfe.gen.tcd.ie/GenomeVx) which allows users to input data either as a list of features and coordinates or as a Since the invention of Sanger sequencing (Sanger et al., 1977), preexisting GenBank flatfile. Because the Postscript format is the cost of DNA sequencing has fallen continually, and the not universally supported, GenomeVx’s output is an Adobe volume of sequence data in public databases has correspond- Portable Document Format file. Although the output from ingly risen (Collins et al., 2003). Thus, we estimate that the GenomeVx can be used directly for presentation (Fig. 1), we number of sequenced organellar genomes from eukaryotes has expect that most users will edit the resulting map with a doubled roughly every two years since the first such sequences program such as Adobe Illustrator. were published (data not shown; Ohyama et al., 1986; Figure 1 illustrates the unedited output from GenomeVx, Shinozaki et al., 1986). Indeed, the number of sequenced using the chloroplast genome sequence of the American angiosperm chloroplast genomes in GenBank tripled from 24 sycamore Platanus occidentalis (Moore et al., 2006) as input. at the end of 2005 to at least 73 at the end of 2007, and new The image shown was created directly from the features in the sequencing technologies are already pushing this number GenBank record for this genome (NC_008335). GenomeVx upward (Moore et al., 2006). does not attempt to correct for the occasional overlaps in One of us (KHW) sequenced one chloroplast genome in 1992 gene names shown, but the labels can be moved manually by and another in 2007. We were surprised to find that, although editing the PDF file. The colors in the Figure were produced the annotation toolkits for organelle genomes had improved automatically: genes are colored based on the first two letters of over this period (Wyman et al., 2004), there were still no easy- the gene name (except for ribosomal RNAs which are all given to-use, free web tools for making publication-quality genomic a single color). maps. Most papers reporting sequences of chloroplast or Input into GenomeVx can either be done manually by mitochondrial genomes include a circular map showing gene pasting genes or nucleotide features (e.g. SNPs) from a locations (Cai et al., 2006; Guo et al., 2007; Saski et al., 2005; program such as Microsoft Excel or by uploading a Talla et al., 2005). However, by making enquiries, we GenBank-format flatfile. When imported from a GenBank discovered that these maps are still often laboriously hand- file, coordinates appear as an editable list in the web interface, drawn, although there are at least three packages which can giving the user the option of overriding the automatic coloring generate them (Gibson and Smith, 2003; Sato and Ehira, 2003; decisions or editing the annotation. The program can also Stothard and Wishart, 2005). With all bioinformatics software there are trade-offs between include miscellaneous features on one or more inner scale rings ease-of-use and the number of features. The three tools (e.g. the inverted repeats in Fig. 1). GenomeVx is intended to simplify the study of organelle genomes by allowing biologists to produce circular genome *To whom correspondence should be addressed. maps without resorting to ad-hoc solutions. The web-based The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org 861 G.C.Conant and K.H.Wolfe Fig. 1. A chloroplast genome map produced by GenomeVx. Genes are colored in groups based on the first two letters of the gene name. A user- specified number of evenly spaced scale indices are produced after rounding the genome size to the nearest two digits (thus, the distance between the last label and 0 kb may be greater than between the other markers). GenomeVx can orient the map either anticlockwise from 3 O’clock (the convention for chloroplast genomes) or clockwise from 12 O’clock (the convention for mitochondrial genomes). Gibson,R. and Smith,D.R. (2003) Genome visualization made fast and simple. interface allows quick access without the installation of local Bioinformatics, 19, 1449–1450. software. We hope that GenomeVx will enable researchers who Guo,X. et al. (2007) Rapid evolutionary change of common bean (Phaseolus study circular genomes to spend less time drawing and more vulgaris L) plastome, and the genomic diversification of legume chloroplasts. time on topics of greater scientific interest. BMC Genomics, 8, 228. Moore,M.J. et al. (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol., 6, 17. Ohyama,K. et al. (1986) Chloroplast gene organization deduced from complete ACKNOWLEDGEMENTS sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature, 322, We thank K. Diekmann, A.C. Frank and J. Mower for 572–574. Sanger,F. et al. (1977) Nucleotide sequence of bacteriophage phi X174 DNA. suggestions during the design and testing of GenomeVx. Nature, 265, 687–695. We also thank K. Byrne and K. Hokamp for technical Saski,C. et al. (2005) Complete chloroplast genome sequence of Gycine max and assistance developing the web interface. This work was comparative analyses with other legume genomes. Plant Mol. Biol., 59, supported by Science Foundation Ireland. 309–322. Sato,N. and Ehira,S. (2003) GenoMap, a circular genome data viewer. Conflict of Interest: none declared. Bioinformatics, 19, 1583–1584. Shinozaki,K. et al. (1986) The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression. EMBO J., 5, 2043–2049. REFERENCES Stothard,P. and Wishart,D.S. (2005) Circular genome visualization and explora- tion using CGView. Bioinformatics, 21, 537–539. Cai,Z. et al. (2006) Complete plastid genome sequences of Drimys, Liriodendron, Talla,E. et al. (2005) The complete mitochondrial genome of the yeast and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol. Biol., 6,77. Kluyveromyces thermotolerans. FEBS Lett., 579, 30–40. Collins,F.S. et al. (2003) The human genome project: lessons from large-scale Wyman,S.K. et al. (2004) Automatic annotation of organellar genomes with biology. Science, 300, 286–290. DOGMA. Bioinformatics, 20, 3252–3255.

Journal

BioinformaticsOxford University Press

Published: Jan 28, 2008

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