computer science

Jpred

Jpred is a computer science 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 Jpred rather than just read about it. In short: Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction, that has existed since 1998 in different versions. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions.

Key takeaways

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

Reference excerpt

Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction, that has existed since 1998 in different versions. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 134 000 jobs per month and has carried out over 2 million predictions in total for users in 179 countries.

JPred 2 The static HTML pages of JPred 2 are still available for reference.

JPred 3 The JPred v3 followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References). This release added new functionality and fixed many bugs. The highlights are:

New, friendlier user interface Retrained and optimised version of Jnet (v2) - mean secondary structure prediction accuracy of >81% Batch submission of jobs Better error checking of input sequences/alignments Predictions now (optionally) returned via e-mail Users may provide their own query names for each submission JPred now makes a prediction even when there are no PSI-BLAST hits to the query PS/PDF output now incorporates all the predictions

JPred 4 The current version of JPred (v4) has the following improvements and updates incorporated:

Retrained on the latest UniRef90 and SCOPe/ASTRAL version of Jnet (v2.3.1) - mean secondary structure prediction accuracy of >82%. Upgraded the Web Server to the latest technologies (Bootstrap framework, JavaScript) and updating the web pages – improving the design and usability through implementing responsive technologies. Added RESTful API and mass-submission and results retrieval scripts - resulting in peak throughput above 20,000 predictions per day. Added prediction jobs monitoring tools. Upgraded the results reporting – both, on the web-site, and through the optional email summary reports: improved batch submission, added results summary preview through Jalview results visualization summary in SVG and adding full multiple sequence alignments into the reports. Improved help-pages, incorporating tool-tips, and adding one-page step-by-step tutorials. Sequence residues are categorised or assigned to one of the secondary structure elements, such as alpha-helix, beta-sheet and coiled-coil. Jnet uses two neural networks for its prediction. The first network is fed with a window of 17 residues over each amino acid in the alignment plus a conservation number. It uses a hidden layer of nine nodes and has three output nodes, one for each secondary structure element. The second network is fed with a window of 19 residues (the result of first network) plus the conservation number. It has a hidden layer with nine nodes and has three output nodes.

See also PSIPRED List of protein structure prediction software

References

Worked examples

Example 1 — a first encounter with Jpred

Start with the simplest possible case. Write down what Jpred claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In computer science, 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 Jpred 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 Jpred 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 Jpred

In research: Jpred appears in computer science 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 Jpred 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: Jpred is common in secondary-school and first-year university syllabi. It links to neighbouring topics Artificial neural networks, Structural bioinformatics software, so understanding it makes those chapters shorter.
In everyday life: Look for Jpred 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 Jpred in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Jpred 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 Jpred out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Jpred in simple terms?

Why does Jpred matter?

Because it connects several computer science 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 Jpred?

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 Jpred.