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Proteogenomics (PG) is a recent research trend aiming to utilize the proteome information in the discovery of new genomic features in both eukaryotic and prokaryotic organisms. The proteome information is an incomparable source of translation evidence of the genes. While, the MS/MS based proteomics provides high-throughput peptides-based proteome data. Thus, the MS/MS based peptides-based proteomics became the technology-of-choice for many proteogenomics projects.
 
The Rice Proteogenomics Project (RPP), in the Institute for Advanced Biosciences (IAB) Keio University, aims to improve the genome annotation of the rice following a Proteogenomic approach. The first phase of the project approaches the establishment of the analytical pipelines (experimental and bioinformatics) required for the study and the development of an online database system for the storage of the resultant data.
 
OryzaPG-BD is the rice proteogenomics database developed by the RPP. This version of the database contains the proteome of the rice undifferentiated cultured cells, the corresponding cDNA, Transcript and Genome sequences, the novel proteogenomics features and the updated gene models annotation.
 
The information are provides in three flavors browsing, searching and downloading. Also, the results of the evaluation for each novel peptide and the visualization of the new annotation of each gene model are available in .gff3 and .png formats.
 
For more information about how to use OryzaPG-BD, please visit the About DB page.
 
OryzaPG-DB (v1.0) article: Helmy et al, BMC Plant Biology, 2011, 11:63, doi:10.1186/1471-2229-11-63
OryzaPG-DB (v1.1) article: Helmy et al, Frontiers in Plant Sciences. , 2012, 3:65, doi: 10.3389/fpls.2012.00065
 
 
 
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The Database Currently Contains:

Genes/us-mRNAs: 3973
Proteins/cDNA: 6291
Total Peptides: 18214
Novel Peptides: 166
Genes to Be Revised: 62
   
   
   
 
 
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