OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets
By Marc Lohse, Oliver Drechsel, Sabine Kahlau, Ralph Bock. Nucleic Acids Res., 2013
1,438 citations recorded by the source corpus.
Mitochondria and plastids (chloroplasts) are cell organelles of endosymbiotic origin that possess their own genetic information. Most organellar DNAs map as circular double-stranded genomes. Across the eukaryotic kingdom, organellar genomes display great size variation, ranging from ∼15 to 20 kb (the size of the mitochondrial genome in most animals) to >10 Mb (the size of the mitochondrial genome in some lineages of flowering plants). We have developed OrganellarGenomeDraw (OGDRAW), a suite of software tools that enable users to create high-quality visual representations of both circular and linear annotated genome sequences provided as GenBank files or accession numbers. Although all types of DNA sequences are accepted as input, the software has been specifically optimized to properly depict features of organellar genomes. A recent extension facilitates the plotting of quantitative gene expression data, such as transcript or protein abundance data, directly onto the genome map. OGDRAW has already become widely used and is available as a free web tool (http://ogdraw.mpimp-golm.mpg.de/). The core processing components can be downloaded as a Perl module, thus also allowing for convenient integration into custom processing pipelines.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/6484464614bc310c621f151de30b213cf8fbfac7
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In Molecular Biology
- Stephan Greiner
- Pascal Lehwark
- Peter Poczai
- Ali Amiryousefi
- Jaakko Hyvönen
- Jing Tang
- Shuyu Zheng
- Ralph Bock
Citations in the corpus
- OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes (2019, methodology): “A custom configuration file further allows modifying the colour of a gene and/or the name of the gene product to be displayed in the map (17,19).”
- CPGView: A package for visualizing detailed chloroplast genome structures (2023, neutral): “…(Wyman et al., 2004), CPGAVAS (Liu et al., 2012), Plann (Huang & Cronk, 2015), Verdant (McKain et al., 2017), GeSeq (Tillich et al., 2017 ), AGORA (Jung et al., 2018), OrganellarGenomeDRAW version 1.3.1 (OGDRAW) (Lohse et al., 2013), CPGAVAS2 (Shi et al., 2019), and Chloroplot (Zheng et al., 2020).”
- Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes (2020, methodology): “The default settings for automatic IR detection embedded in OGDRaw assume that IR sequences are completely identical (Lohse et al., 2013); otherwise, the algorithm terminates the search when single nucleotide polymorphisms (SNPs) are encountered in the sequences.”