Nitschké P, Guerdoux-Jamet P, Chiapello H, Faroux G, Hénaut C, Hénaut A, Danchin A
Université de Versailles Saint Quentin, Laboratoire Génome et Informatique, France.
FEMS Microbiol Rev. 1998 Oct;22(4):207-27. doi: 10.1111/j.1574-6976.1998.tb00368.x.
The present article describes a genome database reviewing gene-related knowledge of two model bacteria, Bacillus subtilis and Escherichia coli. The database, Indigo, is open through the World-Wide Web (http://indigo.genetique.uvsq.fr). The concept used for organising the data, the concept of neighbourhood, allows one to explore the database content in an efficient although somewhat unusual way. Here, genes are related to each other by a variety of neighbourhoods, including proximity in the chromosome, phylogenetic kinship, participation in a common metabolic pathway, common presence in an article of the literature, or similar use of the genetic code. Several examples illustrate how this concept of neighbourhood permits one to review the available knowledge about a given gene or gene family, and elaborate unexpected, but revealing, analyses about gene functions.
本文介绍了一个基因组数据库，该数据库回顾了两种模式细菌——枯草芽孢杆菌和大肠杆菌的基因相关知识。这个名为Indigo的数据库通过万维网（http://indigo.genetique.uvsq.fr）开放。用于组织数据的概念，即邻域概念，使人们能够以一种高效但有点不同寻常的方式探索数据库内容。在这里，基因通过多种邻域相互关联，包括在染色体上的邻近性、系统发育亲缘关系、参与共同的代谢途径、在文献文章中的共同出现，或遗传密码的相似使用。几个例子说明了邻域概念如何使人们能够回顾关于给定基因或基因家族的现有知识，并对基因功能进行意想不到但有启发性的分析。
