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  OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

Lohse, M., Drechsel, O., Kahlau, S., & Bock, R. (2013). OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res., 41(Web Server issue), W575-W581. doi:10.1093/nar/gkt289.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-1DE6-D Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-A2AD-4
Genre: Journal Article

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 Creators:
Lohse, M.1, Author              
Drechsel, O.1, Author              
Kahlau, S.2, Author              
Bock, R.2, Author              
Affiliations:
1Integrative Carbon Biology, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753329              
2Organelle Biology and Biotechnology, Department Bock, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753326              

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 Abstract: 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 approximately 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.

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Language(s): eng - English
 Dates: 2013-04-242013
 Publication Status: Published in print
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 Identifiers: Other: 23609545
DOI: 10.1093/nar/gkt289
ISSN: 1362-4962 (Electronic)0305-1048 (Linking)
URI: http://www.ncbi.nlm.nih.gov/pubmed/23609545http://nar.oxfordjournals.org/content/early/2013/04/22/nar.gkt289
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Title: Nucleic Acids Res.
Source Genre: Journal
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Pages: - Volume / Issue: 41 (Web Server issue) Sequence Number: - Start / End Page: W575 - W581 Identifier: -