xiNET: cross-link network maps with residue resolution.
Bottom Line: xiNET is a visualization tool for exploring cross-linking/mass spectrometry results.The interactive maps of the cross-link network that it generates are a type of node-link diagram.In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. xiNET is open source, released under the Apache version 2 license.
Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;Show MeSH
Mentions: In this section, we provide detailed instructions for creating a xiNET map by uploading data to the website (Uploading Data to Website) or, to keep all data fully within the user's control, by using the tool locally (Local Use). We show these maps and then (Further Examples) briefly introduce other examples needed to illustrate all the features of xiNET. Fig. 3 shows the default legend for xiNET, which is used in the output shown.
Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;