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MIPS PlantsDB: a database framework for comparative plant genome research.

Thomas Nussbaumer¹, Mihaela M Martis, Stephan K Roessner

¹Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany.

Nucleic Acids Research

|December 4, 2012

Summary

This summary is machine-generated.

MIPS PlantsDB provides a comprehensive resource for plant genome data, integrating model and crop species. It offers comparative genomics tools to aid researchers in interpreting complex plant genomic information.

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Area of Science:

Genomics
Bioinformatics
Plant Science

Background:

The exponential growth in plant genome sequencing data necessitates structured information resources.
Databases are crucial for both model and crop plants, requiring intuitive access and comparative tools.
MIPS PlantsDB was established to address these needs for integrative and comparative plant genome research.

Purpose of the Study:

To present MIPS PlantsDB as an updated, comprehensive resource for plant genome research.
To highlight the integration of comparative genomics tools for analyzing plant genomes.
To showcase novel analyses of complex genomes, particularly within the Triticeae species.

Main Methods:

Development and maintenance of database instances for multiple plant species (e.g., Arabidopsis, rice, wheat).
Integration of comparative genomics tools like CrowsNest for synteny visualization.
Application of advanced genome analysis strategies for repetitive plant genomes.

Main Results:

PlantsDB currently includes database instances for key plant species, facilitating comparative genomics.
CrowsNest enables visualization and investigation of syntenic relationships, particularly among monocot genomes.
Novel analyses of complex Triticeae genomes are provided and cross-linked with model species data.

Conclusions:

MIPS PlantsDB serves as a vital, integrated resource for plant genome research.
The platform supports comparative analyses across diverse plant species, including crop and model organisms.
Enhanced tools and data integration within PlantsDB empower researchers to interpret complex genomic information effectively.