Plant Physiol.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
QUICK SEARCH:   [advanced]


     

Plant Physiology Preview
Published on May 15, 2009; 10.1104/pp.109.138214

OPEN ACCESS ARTICLE
This Article
Free via Open Access: OA
Right arrow Full Text (Plant Physiology Preview (PDF))
Right arrow Supplemental Data
Right arrowOA All Versions of this Article:
150/3/1135    most recent
pp.109.138214v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Mochida, K.
Right arrow Articles by Shinozaki, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Mochida, K.
Right arrow Articles by Shinozaki, K.
Agricola
Right arrow Articles by Mochida, K.
Right arrow Articles by Shinozaki, K.

Received March 7, 2009
Accepted May 8, 2009

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

Keiichi Mochida , Takuhiro Yoshida , Tetsuya Sakurai , Yasunari Ogihara , and Kazuo Shinozaki *

Plant Science Center, RIKEN, Yokohama 230-0045, Japan; Kihara Institute for Biological Research, Yokohama City University, Yokohama 710-0046, Japan

* Corresponding author; email: sinozaki{at}rtc.riken.go.jp.

The Triticeae Full-Length Coding Sequence (CDS) Database (TriFLDB) contains available information regarding full-length CDSs of the Triticeae crops wheat (Triticum aestivum) and barley (Hordeum vulgare) and includes functional annotations and comparative genomics features. TriFLDB provides a search interface using keywords for gene function and related Gene Ontology (GO) terms and a similarity search for DNA and deduced translated amino acid sequences to access annotations of Triticeae full-length CDS (TriFLCDS) entries. Annotations consist of similarity search results against several sequence databases and domain structure predictions by InterProScan. The deduced amino acid sequences in TriFLDB are grouped with the proteome datasets for Arabidopsis, rice, and sorghum by hierarchical clustering in stepwise thresholds of sequence identity, providing hierarchical clustering results based on full-length protein sequences. The database also provides sequence similarity results based on comparative mapping of TriFLCDSs onto the rice and sorghum genome sequences, which together with current annotations can be used to predict gene structures for TriFLCDS entries. To provide the possible genetic locations of full-length CDSs, TriFLCDS entries are also assigned to the genetically mapped cDNA sequences of barley and diploid wheat, which are currently accommodated in TriMEDB (Triticeae Mapped EST Database). These relational data are searchable from the search interfaces of both databases. The current TriFLDB contains 15,871 full-length CDSs from barley and wheat and includes putative full-length cDNAs for barley and wheat, which are publicly accessible. This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/.




This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
Y. Yamazaki, R. Akashi, Y. Banno, T. Endo, H. Ezura, K. Fukami-Kobayashi, K. Inaba, T. Isa, K. Kamei, F. Kasai, et al.
NBRP databases: databases of biological resources in Japan
Nucleic Acids Res., November 24, 2009; (2009) gkp996v1.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
ASPB Publications PLANT PHYSIOLOGY® THE PLANT CELL
Copyright © 2009 by the American Society of Plant Biologists