Study on the DNA database and other biological databases

DNA数据库及其他生物数据库的研究

• 批准号: 10041187
• 负责人: GOJOBORI Takashi
• 金额: $ 14.98万
• 依托单位: National Institute of Genetics
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (A).
• 财政年份: 1998
• 资助国家: 日本
• 起止时间: 1998 至 2000
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-10041187/
• 关键词: DDBJ; EMBL; GenBank; NCBI; INSDB; Human genome; bioinformatics; 分子進化; DNA; データベース; タンパク質; Gen Bank

Among the results we obtained in our research, "13th International Nucleotide Sequence Database Collaborators Meeting "is most important. we thus mainly report about that. This meeting was held in Bethesda, Maryland, USA, from May l6 to 18, 2000, As the delegate from DDBJ, Professor Yoshio Tateno (Director of DDBJ), Professor Hideaki Sugawara, Dr. Satoshi Miyazaki and three other DDBJ attended it., and they discussed various problems concerning International Nucleotide Sequence Database with the attendants of NCBI (host) and EBB from Europe. The important matters decided at this meeting are as follows. (1) HTG draft sequence quality score assignment. G5 (The five biggest human genome sequencing centers) required assignment of quality score files to GenBank and EMBL.Because similar request was also made to DDBJ from human genome projects in Japan, we decided to correspond with this matter. (2) DDBJ's proposal for creation of new division (FLI) for full length insert cDNA was accepted. (3) DDBJ's proposal for usage of redefined/transl_table= "11" for the case of plastid in gereral, substituting for universal genetic code, /transl_table= "1" was accepted. (4) EMBL proposed clarification of/exception usage, which had been used without clear rules. DDBJ/GenBank agreed with it. (5) GenBank's proposal for use of only one/gene qualifier and addition of/gene_syn as synonyms was rejected by EMBL and DDBJ.Besides, Dr. Takashi Gojobori and other research staffs visited research institutes related to bioinformatics in USA, Australia, Italy, Germany, and China, and investigated construction of databases for bioinformatics and their current usages.

在我们的研究成果中，“第13届国际核苷酸序列数据库合作者会议”是最重要的。所以我们主要报道这个。这次会议于2000年5月16日至18日在美国马里兰州的贝塞斯达举行，DDBJ的代表，DDBJ主任馆野义雄教授，菅原秀明教授，宫崎智博士和其他三位DDBJ的代表出席了会议。并与NCBI（主办单位）和欧洲EBB的参加者就国际核苷酸序列数据库的有关问题进行了讨论。这次会议决定的重要事项如下。(1)HTG草案序列质量评分分配。G5（五大人类基因组测序中心）要求向GenBank和EMBL分配质量评分文件，由于日本人类基因组计划也向DDBJ提出了类似要求，因此我们决定与之对应。(2)DDBJ提出的为全长插入cDNA创建新的分裂区（FLI）的建议被接受。(3)DDBJ关于在一般情况下使用重新定义的/transl_table=“11”代替通用遗传密码/transl_table=“1”的建议被接受。(4)EMBL建议澄清/例外用法，因为使用时没有明确的规则。DDBJ/GenBank对此表示赞同。（5）GenBank提出的只使用一个/gene限定词和增加/gene_syn作为同义词的建议被EMBL和DDBJ否决。此外，五条堀隆博士和其他研究人员访问了美国、澳大利亚、意大利、德国和中国的生物信息学相关研究机构，考察了生物信息学数据库的建设和使用现状。

项目成果

Bellgard, M.: "Significant differences between the G+C content of synonymous codons in orthologous genes and the genomic G+C content."Gene. 238 1. 33-37 (1999)

Bellgard, M.：“直系同源基因中同义密码子的 G C 含量与基因组 G C 含量之间的显着差异。”基因。

Kikuchi M.: "CAMUS DB : Development of structural database for homology search"Currents in Computational Molecular Biology In Miyano S., Shamir R., and Takagi T.(eds.). 80-81 (2000)

Kikuchi M.：“CAMUS DB：用于同源搜索的结构数据库的开发”计算分子生物学的最新进展，宫野 S.、沙米尔 R. 和高木 T.（编辑）。

Eric S: "Lander Initial sequepcing and analysis of the human genome"Nature. 409 6822. 860-921 (2001)

Eric S：“兰德对人类基因组的初始测序和分析”《自然》。

Kawabata, T.: "The protein mutant database"Nucleic Acids Res.. 27. 355-357 (1999)

Kawabata, T.：“蛋白质突变体数据库”Nucleic Acids Res.. 27. 355-357 (1999)

Yamazaki M.: "Genomic organization around the centromeric end of the HLA class I region : Large-scale sequence analysis" Journal of Molecular Evolution. in press.

Yamazaki M.：“HLA I 类区域着丝粒末端周围的基因组组织：大规模序列分析”分子进化杂志。