Abstract: 

Cytoscape is an open-source program that enables visualization of complex networks that is available as a stand-alone program or as a JavaScript library (Cytoscape.js) for web-based integration. We use Cytoscape to visualize our aptamer clustering algorithm data. Networks of clustered aptamer sequences are drawn using nodes to represent unique aptamer sequences, and edges connect related aptamer sequence nodes. These networks of aptamers can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using Cytoscape provides a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation.