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. 2006 Jul 1;34(Web Server issue):W400-4.
doi: 10.1093/nar/gkl223.

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

Tobias Dezulian  1 , Martin Schaefer, Roland Wiese, Detlef Weigel, Daniel H Huson
Affiliations

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

Tobias Dezulian et al. Nucleic Acids Res. .

Abstract

CrossLink is a versatile tool for the exploration of relationships between RNA sequences. After a parametrization phase, CrossLink delegates the determination of sequence relationships to established tools (BLAST, Vmatch and RNAhybrid) and then constructs a network. Each node in this network represents a sequence and each link represents a match or a set of matches. Match attributes are reflected by graphical attributes of the links and corresponding alignments are displayed on a mouse-click. The distributions of match attributes such as E-value, match length and proportion of identical nucleotides are displayed as histograms. Sequence sets can be highlighted and visibility of designated matches can be suppressed by real-time adjustable thresholds for attribute combinations. Powerful network layout operations (such as spring-embedding algorithms) and navigation capabilities complete the exploration features of this tool. CrossLink can be especially useful in a microRNA context since Vmatch and RNAhybrid are suitable tools for determining the antisense and hybridization relationships, which are decisive for the interaction between microRNAs and their targets. CrossLink is available both online and as a standalone version at http://www-ab.informatik.uni-tuebingen.de/software.

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Figures

Figure 1
Figure 1
Network of sequence sets A (red nodes) and B (blue nodes) with corresponding matches of set MAA, MAB and MBB represented by links in reddish, greenish and bluish colors, respectively.
Figure 2
Figure 2
The visualization options panel for matches in set MAA displaying the histograms associated with each match attribute.
Figure 3
Figure 3
Alignment window showing two separate matches between one pair of sequences.
Figure 4
Figure 4
The visualization color panel, showing custom pattern–color associations in the center.
Figure 5
Figure 5
The visualization window, with an overview area on the top left and a sequence selection panel on the lower left.
See this image and copyright information in PMC

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