Abstract
Mitochondria and plastids are DNA-containing cell organelles whose genomes occur at high copy numbers per cell. Organellar genomes vary greatly in size ranging from approximately 15 kb for some animal mitochondrial genomes to more than 2 Mb for some plant mitochondrial genomes. The vast majority of organellar genomes map as circular molecules that are difficult to illustrate by available commercial or free software tools. Thus, published genome maps are extremely heterogeneous in design, often tediously drawn semi-manually and lack any consensus in display. Here, we present a new web-based tool, OrganellarGenomeDRAW (OGDRAW), which produces high-resolution custom graphical maps of DNA sequences as stored in standard GenBank format entries. GenBank data can be provided as either file uploads or accession numbers. The program is specially optimized for the display of chloroplast and mitochondrial genomes but can also be used to depict other circular DNA sequences. The design of the program core as a Perl module with an object-oriented interface allows easy integration into custom scripts.
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Acknowledgments
We thank Peter Krüger (MPI-MP) for server set-up and administration and many helpful comments on the design of the website. We are grateful to the members of the Bock laboratory for critical testing of OGDRAW and useful suggestions. We wish to acknowledge the creators and contributors to the BioPerl and ImageMagick projects for providing excellent free software tools. This research was supported by grants from the European Union (FP6 Plastomics project LSHG-CT-2003-503238) and by the Max Planck Society.
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Communicated by L. Tomaska.
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Lohse, M., Drechsel, O. & Bock, R. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52, 267–274 (2007). https://doi.org/10.1007/s00294-007-0161-y
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DOI: https://doi.org/10.1007/s00294-007-0161-y