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

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 V...

• Type: Journal
• Year: 2006
• Where: NAR
• Authors: Tobias Dezulian, Martin Schaefer, Roland Wiese, Detlef Weigel, Daniel H. Huson
• Keywords: Crosslink, Match, NAR 2006, Tools