The rice proteogenomics database OryzaPG-DB: development, expansion and new features
Proteogenomics is the utilization of large-scale proteome data in genome annotation refinement. 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 diges...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2012-04-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00065/full |
| _version_ | 1819111481295241216 |
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| author | Mohamed eHelmy Mohamed eHelmy Naoyuki eSugiyama Masaru eTomita Yasushi eIshihama Yasushi eIshihama |
| author_facet | Mohamed eHelmy Mohamed eHelmy Naoyuki eSugiyama Masaru eTomita Yasushi eIshihama Yasushi eIshihama |
| author_sort | Mohamed eHelmy |
| collection | DOAJ |
| description | Proteogenomics is the utilization of large-scale proteome data in genome annotation refinement. 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). |
| first_indexed | 2024-12-22T03:58:18Z |
| format | Article |
| id | doaj.art-0a8a2cc867e14725af51821f459cf978 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-22T03:58:18Z |
| publishDate | 2012-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-0a8a2cc867e14725af51821f459cf9782022-12-21T18:39:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2012-04-01310.3389/fpls.2012.0006523032The rice proteogenomics database OryzaPG-DB: development, expansion and new featuresMohamed eHelmy0Mohamed eHelmy1Naoyuki eSugiyama2Masaru eTomita3Yasushi eIshihama4Yasushi eIshihama5Keio UniversityInstitute for Advanced Biosciences, Keio UniversityInstitute for Advanced Biosciences, Keio UniversityInstitute for Advanced Biosciences, Keio UniversityKyoto UniversityInstitute for Advanced Biosciences, Keio UniversityProteogenomics is the utilization of large-scale proteome data in genome annotation refinement. 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).http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00065/fullProteomicsbioinformaticsdatabasericeLC-MS/MSproteogenomics |
| spellingShingle | Mohamed eHelmy Mohamed eHelmy Naoyuki eSugiyama Masaru eTomita Yasushi eIshihama Yasushi eIshihama The rice proteogenomics database OryzaPG-DB: development, expansion and new features Frontiers in Plant Science Proteomics bioinformatics database rice LC-MS/MS proteogenomics |
| title | The rice proteogenomics database OryzaPG-DB: development, expansion and new features |
| title_full | The rice proteogenomics database OryzaPG-DB: development, expansion and new features |
| title_fullStr | The rice proteogenomics database OryzaPG-DB: development, expansion and new features |
| title_full_unstemmed | The rice proteogenomics database OryzaPG-DB: development, expansion and new features |
| title_short | The rice proteogenomics database OryzaPG-DB: development, expansion and new features |
| title_sort | rice proteogenomics database oryzapg db development expansion and new features |
| topic | Proteomics bioinformatics database rice LC-MS/MS proteogenomics |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00065/full |
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