Genomatica: an integrated data management and analysis tool for genome sequencing projects
Genomatica is an integrated software tool designed for helping systematic management of a large number of DNA sequence fragments obtained through a genome sequencing project. Its graphic user-interface also allows users to look, with any magnifying factor, into any position of the specified chromoso...
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| Published in | Genome Informatics Vol. 4; pp. 394 - 401 |
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| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Japanese Society for Bioinformatics
1993
日本バイオインフォマティクス学会 |
| Online Access | Get full text |
| ISSN | 0919-9454 2185-842X |
| DOI | 10.11234/gi1990.4.394 |
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| Abstract | Genomatica is an integrated software tool designed for helping systematic management of a large number of DNA sequence fragments obtained through a genome sequencing project. Its graphic user-interface also allows users to look, with any magnifying factor, into any position of the specified chromosome and to browse various kinds of collected information altogether (including: DNA sequence itself, related gene descriptions, bibliographic references, corresponding GenBank entries, confirmed or putative coding regions, results from homology analysis for the expected protein, RNA genes, clone information, enzyme restriction maps, comments from administrator, private memorandums by user). We are planning to use Genomatica in E. coli (local data compilation mainly managed by Mori), B. subtilis (by Ogasawara), and S. cerevisiae (by Murakami) genome sequencing projects. The Genomatica project was started on 1992 as one of the advanced genome database projects sponsored by Human Genome Center, University of Tokyo. In June 1993, ver. 2.0 which was fully re-designed with NCBI vibrant library was released. Further augmented version Genomatica 2.1 (with several sequence analysis functions and network communication modules) will be released on Nov. 1993 and will be distributed through anonymous ftp services. The Genomatica system is currently available for X11 window system on Unix workstations, but Macintosh and IBM-PC versions will be also announced soon. |
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| AbstractList | Genomatica is an integrated software tool designed for helping systematic management of a large number of DNA sequence fragments obtained through a genome sequencing project. Its graphic user-interface also allows users to look, with any magnifying factor, into any position of the specified chromosome and to browse various kinds of collected information altogether (including: DNA sequence itself, related gene descriptions, bibliographic references, corresponding GenBank entries, confirmed or putative coding regions, results from homology analysis for the expected protein, RNA genes, clone information, enzyme restriction maps, comments from administrator, private memorandums by user). We are planning to use Genomatica in E. coli (local data compilation mainly managed by Mori), B. subtilis (by Ogasawara), and S. cerevisiae (by Murakami) genome sequencing projects. The Genomatica project was started on 1992 as one of the advanced genome database projects sponsored by Human Genome Center, University of Tokyo. In June 1993, ver. 2.0 which was fully re-designed with NCBI vibrant library was released. Further augmented version Genomatica 2.1 (with several sequence analysis functions and network communication modules) will be released on Nov. 1993 and will be distributed through anonymous ftp services. The Genomatica system is currently available for X11 window system on Unix workstations, but Macintosh and IBM-PC versions will be also announced soon. |
| Author | Ogasawara, Naoki Akiyama, Yutaka Murakami, Yasufumi Miyajima, Nobuyuki Sato, Kenji Furukawa, Tetsuya Mori, Hirotada Kuhara, Satoru |
| Author_FL | 佐藤 賢二 小笠原 直毅 久原 哲 古川 哲也 森 浩禎 村上 康文 宮嶋 伸行 秋山 泰 |
| Author_FL_xml | – sequence: 1 fullname: 秋山 泰 – sequence: 2 fullname: 森 浩禎 – sequence: 3 fullname: 久原 哲 – sequence: 4 fullname: 小笠原 直毅 – sequence: 5 fullname: 宮嶋 伸行 – sequence: 6 fullname: 古川 哲也 – sequence: 7 fullname: 佐藤 賢二 – sequence: 8 fullname: 村上 康文 |
| Author_xml | – sequence: 1 fullname: Sato, Kenji organization: Department of Information Engineering, Kyushu University – sequence: 1 fullname: Miyajima, Nobuyuki organization: Kazusa DNA Institute – sequence: 1 fullname: Furukawa, Tetsuya organization: Computer Center, Kyushu University – sequence: 1 fullname: Murakami, Yasufumi organization: RIKEN Tsukuba Life Science Center – sequence: 1 fullname: Ogasawara, Naoki organization: Advanced Institute for Science and Technology – sequence: 1 fullname: Mori, Hirotada organization: Advanced Institute for Science and Technology – sequence: 1 fullname: Kuhara, Satoru organization: School of Genetic Resource and Technology, Kyushu University – sequence: 1 fullname: Akiyama, Yutaka organization: Institute for Chemical Research, Kyoto University |
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| References | [1] Rudd, K. E., Miller, W., Ostell, J., Benson, D. A.: Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map, Nucleic Acids Res., 18, 2, 313-321, (1990). [5] Shin, D., Lee, C., Zhang, J., Rudd, K. E., Berg, C. M.: Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system, CABIOS, 8, 3, 227-238, (1992). [3] Miller W., Ostell J., Rudd, K. E.: An algorithm for searching restriction maps, CABIOS, 6, 3, 247-252, (1990). [4] Bouffard, G., Ostell, J., Rudd, K. E.: GeneScape: a relational database of Escherichia coli genomic map data for Macintosh computers, CABIOS, 8, 6, 563-567, (1992). [6] Rouxel, T., Danchin, A., Henaut, A.: METALGEN. DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database, CABIOS, 9, 3, 315-324, (1993). [2] Rudd, K. E., Miller, W., Werner C., Ostell, J., Tolstoshev, C., Satterfield, S.: Mapping sequenced E. coli genes by computer: software, strategies and examples, Nucleic Acids Res., 19, 3, 313-321, (1990). [7] Yura, T., Mori, H., Nagai, H., Nagata, T., Ishihama, A., Fujita, N., Isono K., Mizobuchi, K. and Nakata, A.: Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region, Nucleic Acids Res., 20, 3305-3308, (1992). |
| References_xml | – reference: [5] Shin, D., Lee, C., Zhang, J., Rudd, K. E., Berg, C. M.: Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system, CABIOS, 8, 3, 227-238, (1992). – reference: [6] Rouxel, T., Danchin, A., Henaut, A.: METALGEN. DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database, CABIOS, 9, 3, 315-324, (1993). – reference: [4] Bouffard, G., Ostell, J., Rudd, K. E.: GeneScape: a relational database of Escherichia coli genomic map data for Macintosh computers, CABIOS, 8, 6, 563-567, (1992). – reference: [7] Yura, T., Mori, H., Nagai, H., Nagata, T., Ishihama, A., Fujita, N., Isono K., Mizobuchi, K. and Nakata, A.: Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region, Nucleic Acids Res., 20, 3305-3308, (1992). – reference: [2] Rudd, K. E., Miller, W., Werner C., Ostell, J., Tolstoshev, C., Satterfield, S.: Mapping sequenced E. coli genes by computer: software, strategies and examples, Nucleic Acids Res., 19, 3, 313-321, (1990). – reference: [1] Rudd, K. E., Miller, W., Ostell, J., Benson, D. A.: Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map, Nucleic Acids Res., 18, 2, 313-321, (1990). – reference: [3] Miller W., Ostell J., Rudd, K. E.: An algorithm for searching restriction maps, CABIOS, 6, 3, 247-252, (1990). |
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| Title | Genomatica: an integrated data management and analysis tool for genome sequencing projects |
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