title: The Rice PIPELINE: a unification tool for plant functional genomics.
abstract: The Rice Genome Research Project in Japan performs genome sequencing and comprehensive expression profiling, constructs genetic and physical maps, collects full-length cDNAs and generates mutant lines, all aimed at improving the breeding of the rice plant as a food source. The National Institute of Agrobiological Sciences in Tsukuba, Japan, has accumulated numerous rice biological resources and has already successfully produced a high-quality genome sequence, a high-density genetic map with 3000 markers, 30,000 full-length cDNAs, over 700 expression profiles with a 9000 cDNA microarray and 15,000 flanking sequences with Tos17 insertions in about 3765 mutant lines from about 50,000 transposon insertion lines. These resources are available in the public domain. A new unification tool for functional genomics, called Rice PIPELINE, has also been developed for the dynamic collection and compilation of genomics data (genome sequences, full-length cDNAs, gene expression profiles, mutant lines, cis elements) from various databases. The mission of Rice PIPELINE is to provide a unique scientific resource that pools publicly available rice genomic data for search by clone sequence, clone name, GenBank accession number, or keyword. The web-based form of Rice PIPELINE is available at http://cdna01.dna.affrc.go.jp/PIPE/.
authors.affiliation: Department of Molecular Biology, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Junshi
authors.initials: J
authors.lastname: Yazaki
authors.forename: Keiichi
authors.initials: K
authors.lastname: Kojima
authors.forename: Kouji
authors.initials: K
authors.lastname: Suzuki
authors.forename: Naoki
authors.initials: N
authors.lastname: Kishimoto
authors.forename: Shoshi
authors.initials: S
authors.lastname: Kikuchi
mesh_terms: D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018745:Genome, Plant; D023281:Genomics; D016247:Information Storage and Retrieval; D020407:Internet; D007564:Japan; D009154:Mutation; D012275:Oryza / Q000235:genetics*
chemical_list: D018076:DNA, Complementary