CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality.
The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36,034 unique sequences, but for higher usability it covers 89,683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10,000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5.
Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan. endo@ibio.jp
Toshinori
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Endo
Keisuke
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Ueno
Kouki
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Yonezawa
Katsuhiko
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Mineta
Kohji
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Hotta
Yutaka
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Satou
Lixy
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Yamada
Michio
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Ogasawara
Hiroki
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Takahashi
Ayako
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Nakajima
Mia
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Nakachi
Mamoru
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Nomura
Junko
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Yaguchi
Yasunori
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Sasakura
Chisato
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Yamasaki
Miho
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Sera
Akiyasu C
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Yoshizawa
Tadashi
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Imanishi
Hisaaki
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Taniguchi
Kazuo
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Inaba
D000595:Amino Acid Sequence; D000818:Animals; D002938:Ciona intestinalis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D019295:Computational Biology; D003196:Computer Graphics; D030562:Databases, Protein; D020869:Gene Expression Profiling; D023281:Genomics; D058977:Molecular Sequence Annotation; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D018511:Systems Integration; D014584:User-Computer Interface
D020543:Proteome