A Bioinformatics Resource for Crop Functional Genomics: GFSelector Module in Automated Annotation System, RiceGAAS:GFSelector Module in Automated Annotation System, RiceGAAS

Japan Agricultural Research Quarterly
ISSN 00213551
NII recode ID (NCID) AA0068709X
Full text
43-02-04.pdf1.44 MB

GFSelector (Gene Function Selector, http://alnilam.mi.mss.co.jp/rgadb/) has been developed to perform computational classification of gene models and assignment of unique biological function. It has been incorporated in RiceGAAS (http://ricegaas.dna.affrc.go.jp/usr/) which was designed to provide an analysis pipeline for user submitted genome sequences and comprehensive database for all rice gene models. The combined system facilitates accurate modelling of predicted rice genes, classification of gene structure, and assigning of function and GO (gene ontology) terms to the gene models. The reliability and accuracy are enhanced by integrating several reference databases into the system and generating multiple candidates for determining the function of the gene models. The pipeline is also fully automated thereby facilitating regularly updates of the rice gene models using the latest reference databases. Annotation of soybean, wheat and banana BAC (bacterial artificial chromosome) sequences was performed to test the applicability of the pipeline to other crops. As compared with the GenBank CDS (coding sequence) features, more than 83% of nucleotide-level sensitivity was obtained for the gene modelling by the pipeline. It was also confirmed that 95% of functional annotation by the pipeline was nearly equal or better than the corresponding GenBank CDS feature.

Date of issued
Creator SAKATA Katsumi IKAWA Hiroshi WATANABE Hiroyuki ASHIKAWA Ikuo SHIMIZU Yuji HORIUCHI Ikuo ANTONIO Baltazar A. NUMA Hisataka NAGAMURA Yoshiaki MATSUMOTO Takashi
Subject

database

gene ontology

web-based system

Publisher Japan International Research Center for Agricultural Sciences
Available Online
NII resource type vocabulary Journal Article
Volume 43
Issue 2
spage 103
epage 113
DOI 10.6090/jarq.43.103
Rights Japan International Research Center for Agricultural Sciences
Language eng

Related Publication