Dezulian Tobias, Schaefer Martin, Wiese Roland, Weigel Detlef, Huson Daniel H
Department of Algorithms in Bioinformatics, Center for Bioinformatics Tübingen, Tübingen University, D-72076 Tübingen, Germany.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W400-4. doi: 10.1093/nar/gkl223.
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.
CrossLink是一种用于探索RNA序列之间关系的多功能工具。在参数化阶段之后，CrossLink将序列关系的确定委托给已有的工具（BLAST、Vmatch和RNAhybrid），然后构建一个网络。该网络中的每个节点代表一个序列，每条链接代表一个匹配或一组匹配。匹配属性通过链接的图形属性反映，相应的比对在鼠标点击时显示。诸如E值、匹配长度和相同核苷酸比例等匹配属性的分布以直方图形式显示。通过对属性组合进行实时可调阈值设置，可以突出显示序列集并抑制指定匹配的可见性。强大的网络布局操作（如弹簧嵌入算法）和导航功能完善了该工具的探索特性。由于Vmatch和RNAhybrid是用于确定反义关系和杂交关系的合适工具，而这些关系对于微小RNA与其靶标的相互作用至关重要，因此CrossLink在微小RNA的背景下可能特别有用。CrossLink既可以在线获取，也可以从http://www-ab.informatik.uni-tuebingen.de/software获得独立版本。
