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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
We describe GenomeVx, a web-based tool for making editable,
publication-quality, maps of mitochondrial and chloroplast genomes
and of large plasmids. These maps show the location of genes and
chromosomal features as well as a position scale. The program
takes as input either raw feature positions or GenBank records.
In the latter case, features are automatically extracted and colored,
an example of which is given. Output is in the Adobe Portable
Document Format (PDF) and can be edited by programs such as
Adobe Illustrator.
Availability: GenomeVx is available at http://wolfe.gen.tcd.ie/
GenomeVx
Contact: conantg@tcd.ie
Since the invention of Sanger sequencing (Sanger et al., 1977),
the cost of DNA sequencing has fallen continually, and the
volume of sequence data in public databases has correspond-
ingly risen (Collins et al., 2003). Thus, we estimate that the
number of sequenced organellar genomes from eukaryotes has
doubled roughly every two years since the first such sequences
were published (data not shown; Ohyama et al., 1986;
Shinozaki et al., 1986). Indeed, the number of sequenced
angiosperm chloroplast genomes in GenBank tripled from 24
at the end of 2005 to at least 73 at the end of 2007, and new
sequencing technologies are already pushing this number
upward (Moore et al., 2006).
One of us (KHW) sequenced one chloroplast genome in 1992
and another in 2007. We were surprised to find that, although
the annotation toolkits for organelle genomes had improved
over this period (Wyman et al., 2004), there were still no easy-
to-use, free web tools for making publication-quality genomic
maps. Most papers reporting sequences of chloroplast or
mitochondrial genomes include a circular map showing gene
locations (Cai et al., 2006; Guo et al., 2007; Saski et al., 2005;
Talla et al., 2005). However, by making enquiries, we
discovered that these maps are still often laboriously hand-
drawn, although there are at least three packages which can
generate them (Gibson and Smith, 2003; Sato and Ehira, 2003;
Stothard and Wishart, 2005).
With all bioinformatics software there are trade-offs between
ease-of-use and the number of features. The three tools
mentioned above are very feature-rich. However, as a result,
all must be installed locally by the user, and all also have some
combination of local library dependence, complex input
formatting and output formats that are difficult to edit. We
set out to create a simple Web-based tool (GenomeVx) for
making circular maps. This program would not attempt to
duplicate the features available with existing tools; rather it
would aim to be as simple-to-use as possible, with a web-based
interface and an output format which would be accessible on
almost all hardware platforms.
Our initial Postscript maps are generated by a Cþþ program
linked to the GNU plotutils package (http://www.gnu.org/
software/plotutils/). This program is wrapped into a CGI front-
end (http://wolfe.gen.tcd.ie/GenomeVx) which allows users to
input data either as a list of features and coordinates or as a
preexisting GenBank flatfile. Because the Postscript format is
not universally supported, GenomeVx’s output is an Adobe
Portable Document Format file. Although the output from
GenomeVx can be used directly for presentation (Fig. 1), we
expect that most users will edit the resulting map with a
program such as Adobe Illustrator.
Figure 1 illustrates the unedited output from GenomeVx,
using the chloroplast genome sequence of the American
sycamore Platanus occidentalis (Moore et al., 2006) as input.
The image shown was created directly from the features in the
GenBank record for this genome (NC_008335). GenomeVx
does not attempt to correct for the occasional overlaps in
gene names shown, but the labels can be moved manually by
editing the PDF file. The colors in the Figure were produced
automatically: genes are colored based on the first two letters of
the gene name (except for ribosomal RNAs which are all given
a single color).
Input into GenomeVx can either be done manually by
pasting genes or nucleotide features (e.g. SNPs) from a
program such as Microsoft Excel or by uploading a
GenBank-format flatfile. When imported from a GenBank
file, coordinates appear as an editable list in the web interface,
giving the user the option of overriding the automatic coloring
decisions or editing the annotation. The program can also
include miscellaneous features on one or more inner scale rings
(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
maps without resorting to ad-hoc solutions. The web-based
*To whom correspondence should be addressed.
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interface allows quick access without the installation of local
software. We hope that GenomeVx will enable researchers who
study circular genomes to spend less time drawing and more
time on topics of greater scientific interest.
ACKNOWLEDGEMENTS
We thank K. Diekmann, A.C. Frank and J. Mower for
suggestions during the design and testing of GenomeVx.
We also thank K. Byrne and K. Hokamp for technical
assistance developing the web interface. This work was
supported by Science Foundation Ireland.
Conflict of Interest: none declared.
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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).
G.C.Conant and K.H.Wolfe
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