biology

TargetScan

TargetScan is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand TargetScan rather than just read about it. In short: In bioinformatics, TargetScan is a web server that predicts biological targets of microRNAs (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.

Key takeaways

TargetScan belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect TargetScan to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of TargetScan from memory before moving on to harder problems.

Reference excerpt

In bioinformatics, TargetScan is a web server that predicts biological targets of microRNAs (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 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, Drosophila melanogaster, and Caenorhabditis elegans, 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 (PCT 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 and zebrafish mRNA models for which 3' untranslated regions (3' UTRs) are defined using polyadenylation sites that are experimentally determined using accurate high-throughput methods.

References

External links TargetScan miRBase Bartel Lab

Worked examples

Example 1 — a first encounter with TargetScan

Start with the simplest possible case. Write down what TargetScan claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to TargetScan before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about TargetScan ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of TargetScan

In research: TargetScan appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses TargetScan in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: TargetScan is common in secondary-school and first-year university syllabi. It links to neighbouring topics Biological databases, MicroRNA, Servers (computing), so understanding it makes those chapters shorter.
In everyday life: Look for TargetScan outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study TargetScan in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what TargetScan means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain TargetScan out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is TargetScan in simple terms?

Why does TargetScan matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study TargetScan?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on TargetScan.