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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
POGs/PlantRBP: a resource for comparative genomics in plants.
Nigel S Walker1, Nicholas Stiffler, Alice Barkan
1Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
Nucleic Acids Research
|December 5, 2006
Summary
The PlantRBP database integrates plant RNA binding protein (RBP) data from rice, Arabidopsis, and maize into putative orthologous groups (POGs). This resource aids in comparative genomics and understanding RBP functions across species.
Area of Science:
- Plant molecular biology
- Bioinformatics
- Comparative genomics
Background:
- RNA binding proteins (RBPs) play crucial roles in gene regulation.
- Understanding RBP evolution and function requires cross-species comparisons.
- Existing databases may lack integrated ortholog information for key plant species.
Purpose of the Study:
- To develop a comprehensive relational database, PlantRBP, for plant RNA binding proteins.
- To facilitate the identification and analysis of orthologous RBPs across rice, Arabidopsis, and maize.
- To provide a resource for exploring RBP domain organization and intracellular targeting predictions.
Main Methods:
- Construction of putative orthologous groups (POGs) using a mutual-best-hit strategy based on BLAST comparisons.
- Integration of complete proteomes from Arabidopsis and rice, and available sequences from maize.
- Annotation of POGs with domain organization, gene models, phylogenetic trees, and targeting predictions.
Main Results:
- The PlantRBP database successfully integrates orthologous RBPs from rice, Arabidopsis, and maize into POGs.
- Detailed annotations including domain organization, phylogenetic trees, and targeting predictions are available for each POG.
- A graphical display enables mapping of maize sequences to their most similar rice orthologs.
Conclusions:
- PlantRBP provides a valuable resource for comparative analysis of plant RBPs.
- The database facilitates research into RBP evolution, function, and conservation across species.
- Query functionalities and integrated data enhance the study of protein domains and cellular localization.
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