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.

我们研究取得的成果中，最重要的是“第十三届国际核苷酸序列数据库合作者会议”。因此我们主要报道这一点。本次会议于2000年5月16日至18日在美国马里兰州贝塞斯达举行，DDBJ所长馆野义夫教授、菅原英明教授、宫崎智博士等3位DDBJ代表作为DDBJ的代表出席了会议。并与来自欧洲的NCBI（东道主）和EBB的与会者讨论了有关国际核苷酸序列数据库的各种问题。本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（五个最大的人类基因组测序中心）要求将质量评分文件分配给 GenBank 和 EMBL。由于日本人类基因组计划也向 DDBJ 提出了类似的要求，因此我们决定对应此事。 (2) DDBJ关于为全长插入cDNA创建新分区(FLI)的建议被接受。 (3) DDBJ关于在一般质体情况下使用redefine/transl_table=“11”代替通用遗传密码/transl_table=“1”的建议被接受。 (4) EMBL提出澄清/例外用法，该用法一直没有明确的规则。 DDBJ/GenBank 对此表示同意。 (5) GenBank提出的仅使用一个/gene限定符并添加/gene_syn作为同义词的建议被EMBL和DDBJ拒绝。此外，Takashi Gojobori博士和其他研究人员访问了美国、澳大利亚、意大利的生物信息学相关研究机构，德国、中国，调查了生物信息学数据库的建设及其当前用途。

项目成果

Nakashima H.: "Gene from nine genomes are separated into their organisms in the dinucleotide composition space"DNA Res.5, 251-259. 5. 251-259 (1998)

Nakashima H.：“来自九个基因组的基因在二核苷酸组成空间中被分离到它们的生物体中”DNA Res.5, 251-259。

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。

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。

OOta S.: "Three Tree : A new method to reconstruct phylogenetic trees" Genome Informatics 1998,Universal Academy Press, Tokyo. 340-341 (1998)

OOta S.：“三棵树：重建系统发育树的新方法”基因组信息学 1998 年，环球学院出版社，东京。

Watanabe, M: "A phosphate-induced gene which promotes Penicillium mediated bioconversion ofcis-propenylphosphonic acid to Fosfomycin"Applied and Environmental Microbiology. 65. 1036-1044 (1999)

Watanabe，M：“磷酸盐诱导的基因，促进青霉菌介导的顺丙烯基膦酸生物转化为磷霉素”应用和环境微生物学。