BioMiner -: modeling, analyzing, and visualizing biochemical pathways and networks
BioMiner -: modeling, analyzing, and visualizing biochemical pathways and networks
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DOI：
10.1093/bioinformatics/18.suppl_2.s219
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发表时间：
2002-10-01
期刊：
影响因子：
5.8
通讯作者：
Lenhof, HP
中科院分区：
文献类型：
--
作者：
Sirava, M;Schäfer, T;Lenhof, HP
动机：了解新测序的生物体的生物化学是后基因组分析的一项基本任务。然而，由于基因组和阵列数据的增长速度比生化信息快得多，因此有必要通过比较分析来推断反应。目前还没有用于此目的的集成且易于使用的软件工具。结果：我们提出了一种新的软件系统 - BioMiner - 用于分析和可视化生化途径和网络。 BioMiner 基于一种新的全面、可扩展和可重用的数据模型 - BioCore - 可用于对生化途径和网络进行建模。作为第一个应用程序，我们推出了 PathFinder，这是一种通过基于序列相似性比较相关生物体组来预测生化途径的新工具。我们通过大量实验成功测试了 PathFinder，例如细菌中经过充分研究的糖酵解。此外，还提供了一个名为 PathViewer 的应用程序，用于代谢网络的可视化。 PathViewer 是我们所知的第一个支持不同生物体代谢网络图形比较的应用程序。 。
Motivation: Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet.Results: We present a new software system-BioMiner-for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model-BioCore-which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms. .