In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [M. Rehmsmeier, P. Steffen, M. Höchsmann and R. Giegerich (2004) RNA, 10, 1507-1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G:U base...

MicroRNAs (miRNAs) are short RNAs that post-transcriptionally regulate the expression of target genes by binding to the target mRNAs. Although a large number of animal miRNAs has been defined, only a few targets are known. In contrast to plant miRNAs, which usually bind nearly perfectly to their targets, animal miRNAs bind less tightly, with a few nucleotides being unbound, thus producing more ...

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 reflect...

MOTIVATION Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. Additionally ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecule...

MicroRNAs (miRNAs) are 20-24 nt long endogenous non-coding RNAs that act as post-transcriptional regulators in metazoa and plants. Plant miRNA targets typically contain a single sequence motif with near-perfect complementarity to the miRNA. Here, we extended and applied the program RNAhybrid to identify novel miRNA targets in the complete annotated Arabidopsis thaliana transcriptome. RNAhybrid ...

BACKGROUND To profile the expression of microRNAs (miRNAs) and their potential target genes in the gracilis muscles following ischemic injury in rats by monitoring miRNA and mRNA expression on a genome-wide basis. METHODS Following 4 h of ischemia and subsequent reperfusion for 4 h of the gracilis muscles, the specimens were analyzed with an Agilent rat miRNA array to detect the expressed miR...

Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncRNAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNA...

MiRNAs participate in gene regulation of translation. Some studies have investigated the interactions between genes and intragenic miRNAs. It is important to study the miRNA binding sites of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid programmes were used to compute the hybridization free energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%, and 39.7% of miRNA bindi...

A variety of strategies has been proposed for computationally predicting microRNA target genes (see [1-4] for review). One important methodology uses complete annealing of microRNA and mRNA (similar to local alignments), as in miRanda [5], DIANA-microT [6], RNAhybrid [7] and the algorithm by Watanabe et al. [8]. Another methodology uses string matching of the seed region (potentially with an ex...