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
Related in: MedlinePlus
Mentions: Fig. 7 shows ambiguous data displayed in xiNET. Dashed lines are used to indicate the ambiguous links and highlights on mouse-over show the possible alternatives. In Fig. 7 the numbered bars have been expanded (see Table I for user controls) until the sequence of the protein is visible. When xiNET has information on the peptide sequence, its highlights both the link and the linked peptide on mouse-over. Hence, in Fig. 7 we can see the specific recurring peptide that is the source of ambiguity. (Interactive figure at http://crosslinkviewer.org/figure7.html.)
Affiliation: From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;