Micale Giovanni, Continella Andrea, Ferro Alfredo, Giugno Rosalba, Pulvirenti Alfredo
Department of Computer Science, University of Pisa, Pisa, 56127, Italy.
Department of Electronics, Information and Bioengineering, Polytechnic University of Milan, Milan, 20133, Italy.
F1000Res. 2014 Jul 1;3:140. doi: 10.12688/f1000research.4537.2. eCollection 2014.
Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithm. GASOLINE starts with the identification of sets of similar nodes, called seeds of the alignment. Alignments are then extended in a greedy manner and finally refined. Both the identification of seeds and the extension of alignments are performed through an iterative Gibbs sampling strategy. GASOLINE is a Cytoscape app for computing and visualizing local alignments, without requiring any post-processing operations. GO terms can be easily attached to the aligned proteins for further functional analysis of alignments. GASOLINE can perform the alignment task in few minutes, even for a large number of input networks.
比较蛋白质相互作用网络可以揭示远缘物种中特定功能或过程的有趣相互作用模式。在本文中，我们介绍了GASOLINE，这是一个用于蛋白质-蛋白质相互作用（PPI）网络多重局部比对的Cytoscape应用程序。该应用程序基于同名的贪婪随机算法。GASOLINE首先识别相似节点集，即比对种子。然后以贪婪方式扩展比对，最后进行优化。种子的识别和比对的扩展均通过迭代吉布斯采样策略执行。GASOLINE是一个用于计算和可视化局部比对的Cytoscape应用程序，无需任何后处理操作。GO术语可以轻松附加到比对的蛋白质上，以便进一步对比对进行功能分析。即使对于大量输入网络，GASOLINE也能在几分钟内完成比对任务。
