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Cytoscape visualization size limit3/29/2023 ![]() ![]() We chose to build a Cytoscape app for GASOLINE because Cytoscape is a very popular tool in bioinformatics and is written in Java, therefore multi-platform. Here, we describe a Cytoscape app based on GASOLINE (Greedy And Stochastic algorithm for Optimal Local alignment of Interaction NEtworks), a greedy and stochastic algorithm for multiple local alignment of PPI networks, introduced inġ5. Cytoscape functionality can be easily extended through Java apps. Cytoscapeġ4 is an open source platform for visualizing and analyzing molecular interaction networks and integrating data with gene expression profiles and other kind of knowledge. Most network alignment algorithms have been provided with their implementations, however none of them is fully integrated within Cytoscape. In local alignment, networks are compared in order to find conserved protein complexes or pathwaysġ3 try to find a complete one-to-one mapping between functional orthologous to infer evolutionary relationships among different species. Alignment methods can be local or global. Network alignment detects functionally orthologous proteins across networks of different species. Among these, PPI networks are important in several biological phenomena such as signaling, transcriptional regulation and formation of multi-enzyme complexesĬomparing PPI networks of evolutionary distant species can help to understand the regulation of a specific function or process, which the sequence comparison alone cannot explainĨ. In the last few years there has been a rapid growth of biological network data, including protein-protein interaction (PPI) networks, metabolic networks and regulatory networksĦ. CONCLUSIONS - A new paragraph describing some interesting applications of GASOLINE, concerning annotation transfer and protein function prediction, was added. Figure 2 was revised, highlighting and describing each panel within GASOLINE app. ![]() RESULTS - The technical characteristics of the machine used for the test were reported. A more detailed description of ISC score was provided. The sentence "GASOLINE is very fast it computes the results on 25 networks in a few minutes" was removed. IMPLEMENTATION - Acronyms for COG, NOG and KOG were defined. A small paragraph describing the main strength and limitations of GASOLINE was added. More details about GASOLINE and its input parameters were included. A small paragraph with a general introduction to Cytoscape and its advantages was included. A new paragraph describing the differences between local and global alignment methods was added. A new paragraph to describe what a network alignment algorithm is and which is the main goal was included. Missing references concerning the available PPI datasets, the most important alignment methods and the importance of using network alignment were added. INTRODUCTION - Acronym for GASOLINE was defined. ABSTRACT - The section was extended with a slightly more detailed description of GASOLINE.
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