The rice proteogenomics database OryzaPG-DB

Development, expansion, and new features

Mohamed Helmy, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS), and mapping of the peptides to their genomic origins and the genomic novelty of each peptide. The sequences of the peptides, proteins, cDNAs and genes, and the gene annotations are available for download in FASTA and GFF3 formats, respectively. Further, an annotated visualization of the gene models, corresponding peptides, and genomic novelty is available for each gene, and MS/MS spectra are available for each peptide. In this article, we discuss the utilization of OryzaPG-DB and report on its development, recent content expansions, and newly added features in the current version (OryzaPG-DB v1.1).

Original languageEnglish
Article number65
JournalFrontiers in Plant Science
Volume3
Issue numberAPR
DOIs
Publication statusPublished - 2012 Apr 2

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peptides
rice
genomics
genes
peptide mapping
rice protein
liquid chromatography
tandem mass spectrometry
proteins

Keywords

  • Bioinformatics
  • Database
  • LC-MS/MS
  • Proteogenomics
  • Proteomics
  • Rice

ASJC Scopus subject areas

  • Plant Science

Cite this

The rice proteogenomics database OryzaPG-DB : Development, expansion, and new features. / Helmy, Mohamed; Sugiyama, Naoyuki; Tomita, Masaru; Ishihama, Yasushi.

In: Frontiers in Plant Science, Vol. 3, No. APR, 65, 02.04.2012.

Research output: Contribution to journalArticle

Helmy, Mohamed ; Sugiyama, Naoyuki ; Tomita, Masaru ; Ishihama, Yasushi. / The rice proteogenomics database OryzaPG-DB : Development, expansion, and new features. In: Frontiers in Plant Science. 2012 ; Vol. 3, No. APR.
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