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A a web tool for the prediction of miRNA targets that is mainly based on the conservation of the potential regulation in plant species. Yes: No: No: Web tool [122] RNA22: The first link (precomputed predictions) provides RNA22 predictions for all protein coding transcripts in human, mouse, roundworm, and fruit fly.
Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competing endogenous RNA (ceRNA) interactions. It is an integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines.
Rna22 is a pattern-based algorithm for the discovery of microRNA target sites and the corresponding heteroduplexes. [1]The algorithm is conceptually distinct from other methods for predicting microRNA:mRNA heteroduplexes in that it does not use experimentally validated heteroduplexes for training, instead relying only on the sequences of known mature miRNAs that are found in the public databases.
[10] which provide predictions for mammals, zebrafish, insects, and nematodes centered on the genes of human, mouse, zebrafish, Drosophila melanogaster, and Caenorhabditis elegans, respectively. Compared to other target-prediction tools [which?] TargetScan provides accurate rankings of the predicted targets for each miRNA. [6]
It is used especially when the read length of the sequencing machine is longer than the sequenced molecule, like the microRNA case. Deconseq Detect and remove contaminations from sequence data. Erne-Filter [ 26 ] is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
[1] [6] StarBase provides miRFunction and ceRNAFunction web tools to predict the function of ncRNAs (miRNAs, lncRNAs, pseudogenes) and protein-coding genes from the miRNA and ceRNA [7] regulatory networks.
Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions [1] [2] with a focus on assessment of RNA target accessibility, [3] for major applications to the rational design of siRNAs [4] in the suppression of gene expressions, and to the identification of targets for regulatory RNAs particularly microRNAs.
MicroRNA (miRNA) is a type of RNA that complementary binds to targeted mRNA sequence to suppress or silence the translation of the mRNA. If the variant disrupts the miRNA target location, the miRNA could have altered binding affinity to the corresponding gene transcript thus changing the mRNA expression level of the transcript.