bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

, TargetScan is a web server that predicts biological targets of

microRNAs Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcri ...

(miRNAs) by searching for the presence of sites that match the seed region of each miRNA. For many species, other types of sites, known as 3'-compensatory sites are also identified. These miRNA target predictions are regularly updated and improved by the laboratory of David Bartel in conjunction with the

Whitehead Institute Whitehead Institute for Biomedical Research is a non-profit research institute located in Cambridge, Massachusetts, United States that is dedicated to improving human health through basic biomedical research. It was founded as a fiscally indep ...

Bioinformatics and Research Computing Group. TargetScan includes TargetScanHuman, TargetScanMouse, TargetScanFish, TargetScanFly, and TargetScanWorm. which provide predictions for mammals, zebrafish, insects, and nematodes centered on the genes of human, mouse,

zebrafish The zebrafish (''Danio rerio'') is a species of freshwater ray-finned fish belonging to the family Danionidae of the order Cypriniformes. Native to South Asia, it is a popular aquarium fish, frequently sold under the trade name zebra danio (an ...

, ''

Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (an insect of the Order (biology), order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the "vinegar fly", "pomace fly" ...

'', and ''

Caenorhabditis elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a Hybrid word, blend of the Greek ''caeno-'' (recent), ''r ...

'', respectively. Compared to other target-prediction tools TargetScan provides accurate rankings of the predicted targets for each miRNA. These rankings are based on either the probability of evolutionarily conserved targeting (P_CT scores.) or the predicted efficacy of repression (context++ scores). Another distinguishing feature of TargetScan is its use of extra mRNA annotations. In particular, TargetScanWorm and TargetScanFish are based on ''

C. elegans ''Caenorhabditis elegans'' () is a free-living transparent nematode about 1 mm in length that lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek ''caeno-'' (recent), ''rhabditis'' ( ...

'' and

mRNA models for which 3' untranslated regions (3' UTRs) are defined using

polyadenylation Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In euka ...

sites that are experimentally determined using accurate high-throughput methods.

References

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External links

TargetScan

miRBase

Bartel Lab
MicroRNA Servers (computing) Biological databases