Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
PLoS One. 2013 Dec 6;8(12):e82210. doi: 10.1371/journal.pone.0082210. eCollection 2013.
The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes.
We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments.
We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.
下一代测序技术极大地提高了微生物基因组测序的通量。为了对新测序的微生物基因组进行功能注释，使用了各种实验和计算方法。整合来自不同来源的信息是增强这种注释的一种强大方法。微生物基因组的功能分析对于下游实验至关重要，但由于目前缺乏适合微生物基因组的信息集成和探索系统，因此受到阻碍。
我们开发了一个数据仓库系统（INDIGO），该系统能够整合注释，以探索和分析新测序的微生物基因组。INDIGO 提供了一个机会，可以从基因组序列到蛋白质结构域、基因本体论和途径水平构建复杂的查询并组合来自多个来源的注释。这个数据仓库旨在从红海细菌和古菌的纯培养物和未培养单细胞的基因组中获取信息。目前，INDIGO 包含了从深海缺氧卤水湖的极端微生物 Salinisphaera shabanensis、Haloplasma contractile 和 Halorhabdus tiamatea 中获取的信息。我们提供了利用该系统深入了解这些生物体独特生活方式和适应极端环境的具体方面的示例。
我们开发了一个数据仓库系统 INDIGO，该系统能够全面整合来自各种资源的信息，用于注释、探索和分析微生物基因组。它将定期更新和扩展新的基因组。它旨在成为一个专门针对红海微生物的资源。此外，通过 INDIGO，我们提供了我们的微生物基因组自动注释（AAMG）管道。INDIGO 网络服务器可在 http://www.cbrc.kaust.edu.sa/indigo 上免费获取。
