The Rice Annotation Project Database (RAP-DB): 2008 update

By Tsuyoshi Tanaka, B. Antonio, S. Kikuchi, T. Matsumoto, Y. Nagamura, H. Numa, H. Sakai, Jianzhon Wu, T. Itoh, Takuji Sasaki and 81 more. Nucleic Acids Res., 2007

342 citations recorded by the source corpus.

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/20cb478e464dec614ff0326f6640e8a8105c4b8d

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In Molecular Biology

1. Xiu-Jie Wang
2. Rasmus Nielsen
3. Karsten Kristiansen
4. Xun Xu
5. Yingrui Li
6. Xin Liu
7. Ryan N. Gutenkunst
8. M. Wang

In Plant Science

1. Rasmus Nielsen
2. Takuji Sasaki
3. Susan McCouch
4. Fumin Zhang
5. Song Ge
6. Ning Jiang
7. Shujun Ou
8. M. Thomson

Citations in the corpus

• MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences (2010, methodology): “The build five rice IRGSP/RAP genome sequence was used (28) as was Repbase version 14.”
• Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes (2011, background): “63. Tanaka, T. et al. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res. 36, D1028–D1033 (2008).”
• PsRobot: a web-based plant small RNA meta-analysis toolbox (2012, methodology): “The Arabidopsis thaliana genome was downloaded from the Arabidopsis Information Resource (TAIR) (24) and the rice genome was from Rice Genome Annotation Project (RGAP) (25) and the Rice Annotation Project Database (RAP-DB) (26) databases.”
• Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics (2013, methodology): “Since the release of the International Rice Genome Sequencing Project (IRGSP) build 4 assembly (Tanaka et al. 2008), the rice genome assembly has been updated twice.”