Lombardot Thierry, Kottmann Renzo, Giuliani Gregory, de Bono Andrea, Addor Nans, Glöckner Frank Oliver
Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany.
BMC Bioinformatics. 2007 Oct 22;8:406. doi: 10.1186/1471-2105-8-406.
Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenomes of environmental relevance must take into account the corresponding habitat (contextual) data, e.g. water depth, physical and chemical parameters. The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis.
We implemented the MetaLook software for visualisation and analysis of marine ecological genomic and metagenomic data with respect to habitat parameters. MetaLook offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a centralised georeferenced database. The user can define environmental containers to organise the sequences according to different habitat criteria. To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported sequences, using the BLAST algorithm. This allows an interactive assessment of the distribution of gene functions in the environment.
MetaLook allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. This software is a step towards the creation of specialised tools to study constrained distributions and habitat specificity of genes correlated with specific processes. MetaLook is available at: http://www.megx.net/metalook.
海洋生态基因组学可定义为应用基因组科学来理解海洋生态系统的结构和功能。在这一研究领域，对具有环境相关性的基因组和宏基因组进行分析时，必须考虑相应的栖息地（背景）数据，如水深、物理和化学参数。创建专门的软件工具和数据库对于实现这种新型的综合分析是必不可少的。
我们实现了MetaLook软件，用于针对栖息地参数对海洋生态基因组和宏基因组数据进行可视化和分析。MetaLook提供了一个三维用户界面，基于一个集中式地理参考数据库，在世界地图上交互式地可视化DNA序列。用户可以定义环境容器，根据不同的栖息地标准来组织序列。为了找到相似序列，可以使用BLAST算法，用地理参考数据库中的基因或用户导入的序列对这些容器进行查询。这使得能够对环境中基因功能的分布进行交互式评估。
MetaLook使科学家能够在环境背景下研究序列数据，并探索基因与栖息地参数之间的相关性。该软件朝着创建专门工具迈出了一步，用于研究与特定过程相关的基因的受限分布和栖息地特异性。可通过以下网址获取MetaLook：http://www.megx.net/metalook。
