title: UTGB/medaka: genomic resource database for medaka biology.
abstract: Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142,414 bacterial artificial chromosome (BAC) and 217,344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16,519,460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5'-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/.
authors.affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan.
authors.forename: Budrul
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authors.lastname: Yamada
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authors.lastname: Kasahara
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authors.lastname: Sasaki
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authors.lastname: Shimada
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authors.forename: Atsushi
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authors.lastname: Toyoda
authors.forename: Yoko
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authors.lastname: Fujiyama
authors.forename: Takashi
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authors.lastname: Sasaki
authors.forename: Atsushi
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authors.lastname: Shimizu
authors.forename: Shuichi
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authors.lastname: Asakawa
authors.forename: Nobuyoshi
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authors.lastname: Shimizu
authors.forename: Shin-ichi
authors.initials: S
authors.lastname: Hashimoto
authors.forename: Jun
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authors.lastname: Yang
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Lee
authors.forename: Kouji
authors.initials: K
authors.lastname: Matsushima
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Sakaizumi
authors.forename: Takanori
authors.initials: T
authors.lastname: Narita
authors.forename: Kazuko
authors.initials: K
authors.lastname: Ohishi
authors.forename: Shinobu
authors.initials: S
authors.lastname: Haga
authors.forename: Fumiko
authors.initials: F
authors.lastname: Ohta
authors.forename: Hisayo
authors.initials: H
authors.lastname: Nomoto
authors.forename: Keiko
authors.initials: K
authors.lastname: Nogata
authors.forename: Tomomi
authors.initials: T
authors.lastname: Morishita
authors.forename: Tomoko
authors.initials: T
authors.lastname: Endo
authors.forename: Tadasu
authors.initials: T
authors.lastname: Shin-I
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Takeda
authors.forename: Yuji
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authors.lastname: Kohara
authors.forename: Shinichi
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authors.lastname: Morishita
mesh_terms: D000818:Animals; D022202:Chromosomes, Artificial, Bacterial; D030541:Databases, Genetic; D015870:Gene Expression; D005819:Genetic Markers; D014644:Genetic Variation; D023281:Genomics; D020407:Internet; D009990:Oryzias / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D024363:Transcription Initiation Site; D014584:User-Computer Interface
chemical_list: D005819:Genetic Markers