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CrossLink: visualization and exploration of sequence relationships between (micro) RNAs

By Tobias Dezulian, Martin Schaefer, Roland Wiese, Detlef Weigel and Daniel H. Huson. With contributions from Norman Warthmann, Rebecca Schwab, Heike Wollmann and Matthias Zschunke.

CrossLink makes extensive use of the yFiles library courtesy of the yWorks diagramming company, the Vmatch sequence analysis software courtesy of Stefan Kurtz, the RNAhybrid MFE hybridisation software by Marc Rehmsmeier et al. and the Basic Local Alignment Search Tool (BLAST) courtesy of the NCBI.

CrossLink is a versatile tool for the exploration of relationships between RNA sequences. After a parametrization phase, CrossLink uses the established tools BLAST, Vmatch and RNAhybrid to determine sequence relationships. Then, nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. Relationship attributes are reflected by labels and graphical attributes of each link and corresponding alignments pop up on a mouse-click. The type and number of links displayed can be adjusted interactively using value histograms and thresholds - taking a combination of dependencies on different relationship aspects into account. Powerful network layout operations and navigation capabilities complete the visualization features of this tool.

One may find CrossLink especially useful in a microRNA context since Vmatch and RNAhybrid are suitable tools for determining antisense and hybridisation relationships which are decisive for the interaction between microRNAs and their targets.

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