title: RiceGAAS: an automated annotation system and database for rice genome sequence.
abstract: An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.
authors.affiliation: National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan. ksakata@nias.affrc.go.jp
authors.forename: Katsumi
authors.initials: K
authors.lastname: Sakata
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
authors.forename: Hisataka
authors.initials: H
authors.lastname: Numa
authors.forename: Baltazar A
authors.initials: BA
authors.lastname: Antonio
authors.forename: Hideki
authors.initials: H
authors.lastname: Nagasaki
authors.forename: Atsuko
authors.initials: A
authors.lastname: Idonuma
authors.forename: Wakako
authors.initials: W
authors.lastname: Watanabe
authors.forename: Yuji
authors.initials: Y
authors.lastname: Shimizu
authors.forename: Ikuo
authors.initials: I
authors.lastname: Horiuchi
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
authors.forename: Kenichi
authors.initials: K
authors.lastname: Higo
mesh_terms: D001331:Automation; D003196:Computer Graphics; D018744:DNA, Plant / Q000235:genetics; D003628:Database Management Systems; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D005544:Forecasting; D017343:Genes, Plant; D018745:Genome, Plant; D016247:Information Storage and Retrieval; D020407:Internet; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins