UTGB/medaka: genomic resource database for medaka biology.
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/.
Ahsan
Budrul
B
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan.
Kobayashi
Daisuke
D
Yamada
Tomoyuki
T
Kasahara
Masahiro
M
Sasaki
Shin
S
Saito
Taro L
TL
Nagayasu
Yukinobu
Y
Doi
Koichiro
K
Nakatani
Yoichiro
Y
Qu
Wei
W
Jindo
Tomoko
T
Shimada
Atsuko
A
Naruse
Kiyoshi
K
Toyoda
Atsushi
A
Kuroki
Yoko
Y
Fujiyama
Asao
A
Sasaki
Takashi
T
Shimizu
Atsushi
A
Asakawa
Shuichi
S
Shimizu
Nobuyoshi
N
Hashimoto
Shin-ichi
S
Yang
Jun
J
Lee
Yongjun
Y
Matsushima
Kouji
K
Sugano
Sumio
S
Sakaizumi
Mitsuru
M
Narita
Takanori
T
Ohishi
Kazuko
K
Haga
Shinobu
S
Ohta
Fumiko
F
Nomoto
Hisayo
H
Nogata
Keiko
K
Morishita
Tomomi
T
Endo
Tomoko
T
Shin-I
Tadasu
T
Takeda
Hiroyuki
H
Kohara
Yuji
Y
Morishita
Shinichi
S
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
D005819:Genetic Markers