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. 2013 Jan;41(Database issue):D1144-51.
doi: 10.1093/nar/gks1153. Epub 2012 Nov 29.

MIPS PlantsDB: A Database Framework for Comparative Plant Genome Research

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Free PMC article

MIPS PlantsDB: A Database Framework for Comparative Plant Genome Research

Thomas Nussbaumer et al. Nucleic Acids Res. .
Free PMC article

Abstract

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

Figures

Figure 1.
Figure 1.
Barley GenomeZipper in MIPS PlantsDB. This figure shows a region on barley chromosome 1 H, constructed with the GenomeZipper concept. Detailed information and sequence download for anchored barley markers as well as ‘zipped’ reference organism genes, barley fl-cDNAs, ESTs and sequence reads can be obtained by clicking the individual links.
Figure 2.
Figure 2.
Visualization of the barley physical map in CrowsNest. A fingerprinted contig (FPC; example ‘contig_20’), consisting of overlapping BAC clones. The different colors depict the anchoring evidence to one of the seven (14) barley chromosomes (chromosome arms). Gray-colored elements have no attached chromosome (arm) information. The symbols represent the different anchoring datatypes: circle = BAC hybridization data to the chromosome arms, vertical rectangle = genetic markers, square flanking the ends of a BAC = BES (BAC end sequence).
Figure 3.
Figure 3.
(AF) CrowsNest visualization levels L1–L4. Different visualization levels of the CrowsNest tool for the reference grass organisms—B. distachyon and S. bicolor. The syntenic regions between the organisms can be browsed in a hierarchical way from macro-synteny (A–C) down to micro-synteny views (F). Navigation between the levels is possible by interactively selecting regions of interest in the views (‘click zoom’) or using the navigation bar.

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