目的:蛋白质-蛋白质相互作用(PPI)网络比对已被证明是诊断和预防某些疾病的有效技术。然而,最大化的困难,同时,这两个品质,衡量的良好性比对(拓扑和生物学质量)已导致对齐产生非常不同的比对。因此,在这些不同品质的排列之间进行比较研究是一个巨大的挑战。多目标优化是一种计算机方法,这在这种情况下非常强大,因为这两种相互冲突的品质都被放在一起考虑。使用多目标方法分析每个PPI网络对准器的对准,可以让您可视化对准及其质量的更大图片,得到非常有趣的结论。本文提出了在多目标领域进行全面的PPI网络对准器研究。
方法:研究了每个对准器和所有对准器的对准,并通过Pareto优势方法进行了比较。每个对准器和所有对准器一起针对五种不同对准方案产生的最佳对准显示在帕累托正面图中。稍后,对准器根据拓扑进行排序,生物,以及它们对齐的综合质量。最后,对齐器还根据其平均运行时间进行排名。
结果:关于构建最佳整体对齐的对齐器,我们发现SAlign,梁,萨拉,和HubAlign是最好的选择。此外,最佳拓扑质量的比对由:SANA,对齐,和HubAlign校准器。相反,返回最佳生物质量排列的排列器是:BEAMS,TAME,和波浪。然而,如果有时间限制,建议选择SAlign以获得高拓扑质量比对,而选择PISwap或SAlign对准器以获得高生物质量比对。
结论:建议使用SANA对准器,以获得拓扑质量的最佳对准,最佳生物质量比对的BEAMS,和SAlign的最佳组合拓扑和生物学质量的比对。同时,SANA和BEAMS的运行时间高于平均水平。因此,有人建议,如有必要,由于时间限制,选择其他,更快的对准器,如SAlign或PISwap,其对准也是高质量的。
OBJECTIVE: The protein-protein interaction (PPI) network alignment has proven to be an efficient technique in the diagnosis and prevention of certain diseases. However, the difficulty in maximizing, at the same time, the two qualities that measure the goodness of alignments (topological and biological quality) has led aligners to produce very different alignments. Thus making a comparative
study among alignments of such different qualities a big challenge. Multi-objective optimization is a computer method, which is very powerful in this kind of contexts because both conflicting qualities are considered together. Analysing the alignments of each PPI network aligner with multi-objective methodologies allows you to visualize a bigger picture of the alignments and their qualities, obtaining very interesting conclusions. This paper proposes a comprehensive PPI network aligner
study in the multi-objective domain.
METHODS: Alignments from each aligner and all aligners together were studied and compared to each other via Pareto dominance methodologies. The best alignments produced by each aligner and all aligners together for five different alignment scenarios were displayed in Pareto front graphs. Later, the aligners were ranked according to the topological, biological, and combined quality of their alignments. Finally, the aligners were also ranked based on their average runtimes.
RESULTS: Regarding aligners constructing the best overall alignments, we found that SAlign, BEAMS, SANA, and HubAlign are the best options. Additionally, the alignments of best topological quality are produced by: SANA, SAlign, and HubAlign aligners. On the contrary, the aligners returning the alignments of best biological quality are: BEAMS, TAME, and WAVE. However, if there are time constraints, it is recommended to select SAlign to obtain high topological quality alignments and PISwap or SAlign aligners for high biological quality alignments.
CONCLUSIONS: The use of the SANA aligner is recommended for obtaining the best alignments of topological quality, BEAMS for alignments of the best biological quality, and SAlign for alignments of the best combined topological and biological quality. Simultaneously, SANA and BEAMS have above-average runtimes. Therefore, it is suggested, if necessary due to time restrictions, to choose other, faster aligners like SAlign or PISwap whose alignments are also of high quality.