A Protein Secondary Structure Prediction Server

JPred is a web server that takes a protein sequence or multiple alignment of protein sequences, and from these predicts the location of secondary structures using a neural network called Jnet. The prediction classifies each amino acid residue as belonging to alpha helix ('H'), beta sheet ('E') or not H or E ('-') secondary structures.

JPred also performs predictions of solved accessibility with Jnet and coiled-coil regions via MultiCoil.

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How does JPred work?

The server runs in two modes; single sequence and multiple sequence.

• 1. Multiple sequence: If you already have a set of aligned sequences you may submit them as either MSF, BLC or FASTA format for prediction (link to format examples). Your alignment will be modified so that it does not contain gaps in the first sequence. The first sequence should therefore always be your target sequence.
• 2. Single sequence: For single sequences a multiple alignment is constructed. It is created by the PSI-BLAST algorithm with 3 iterations. Redundant sequences are removed and gaps that have appeared in the query sequence are removed along with the aligned positions in the sequences. The prediction algorithms are then run. Multiple query sequences can be provided in FASTA format using 'Batch Mode' (link to format examples).
• 3. From Jalview: You can also run JPred in single sequence or multiple sequence mode from within the Jalview multiple alignment workbench. See the Jalview manual on www.jalview.org for more details.

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RESTful API (programmable, command line access)

RESTful API is now available in JPred. The RESTful API allows JPred users to submit jobs from the command line (Unix/Linux shell, Terminal window in Mac/Windows OS). For full documentation/tutorial see the following page..

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What do I need to run JPred?

JPred 4 was tested with major browsers (IE, Chrome, Firefox, Safari). Please let us know if you experience any problems (see contacts).

If you wish to use Jalview you will need a browser that supports Java 1.6, this includes most modern browsers.

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Can I still use JPred 3?

Yes. JPred 3 is still available at the following link: http://www.compbio.dundee.ac.uk/jpred. Around 19th Jan 2015 we plan to make the switch of the "official" JPred to v.4. After that JPred 3 would be accessible via http://www.compbio.dundee.ac.uk/jpred3 to allow for smooth transition. Starting January 2015 all upgrades will be performed on JPred 4.

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Can I still use JPred 2?

No. JPred 2 has been disabled. However, all the static HTML pages are available for reference.

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Are there any example files?

Yes: link to format examples

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How long do I have to wait?

That's a hard question to answer as it's dependent on several aspects such as: a) the number of jobs in the queue, b) the load on the server, c) the runtime of your job.

The size of the queue and the load on the server determine a submission's wait time. If both are small, your job will be waiting less than 1 minute. However, if either is large, your job may be waiting a while.

Once a JPred submission is running, it is time limited to three hours. According to our statistics ~95.4% of submissions complete within an hour, and overall average time of a job completion is 15 min.

The main causes of long runtimes are very common sequence motifs and/or long sequences. If you have a very long sequence to analyse check to see if it can be split into domains, as this will probably allow the job to finish in time. Requests for analysis of very long sequences may be sent to us (see contacts), and we may be able to run your request at a lower priority.
Alternatively, you could create your own alignment and submit that to JPred. This will run faster as JPred won't need to create an alignment for you.

So, at best your submission will be completed in a few minutes and at worst it could be over two hours.

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I would like a copy of the server to run locally, where can I download it?

We are planning to release a standalone installation in the near future. Please contact us if you are interested (see contacts) and/or subscribe to JPred announcements (see contacts).

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What are all the output files?

You will find a 'README' file included with the output files. It details the data each file contains.

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That Java viewer is neat, can I have my own copy?

The viewer and editor, Jalview is freely available. It has its own website – see www.jalview.org

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Who sees the data I submit?

Nobody will look at your sequence data, unless there is a specific bug or problem. Every job is given an internal random ID (even if you supply a non-random one yourself) so only you will know what sequence that ID refers to. However, in order to monitor the server, we maintain statistics on the use of the server.

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How do I report problems?

JPred reports most problems directly to the user with details. If there is something that cannot be resolved or any other strange behaviour don't hesitate to contact us, and we'll try our best to help or repair the problem.

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Where did JPred come from?

The original JPred server was the result of a large-scale comparative analysis of secondary structure prediction algorithms (Cuff & Barton, 1999). We developed flexible software to standardise the input and output requirements of the 6 prediction algorithms.

During the analysis, we also found that we needed a quick and effective way to build automatic alignments that would still give good predictions. This led to the development of the automatic method for building multiple sequence alignments and redundancy filters that are used in JPred.

These methods were then replaced by a neural network program called Jnet (Cuff & Barton, 2000), which achieves the same accuracy as the combined prediction programs.

JPred received a major update of the site and of Jnet in 2007, where the mean Q3 prediction accuracy was improved to 81% [ref] (the current prediction accuracy is 82%).

JPred 4 (December 2014) is the latest revision to both the core JNet algorithm and the website.

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What do the characters 'E', 'H', 'B' and '-' represent in the prediction?

They represent extended (E), helical (H) and other (-) types of secondary structure respectively. In the solvent accessibility predictions they represent buried (B) and exposed (-) for each of the 0%, 5% and 25% solvent accessibility cut-offs.

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What do the colours mean in the Postscript/PDF output from JPred?

The postscript is generated by Alscript. The code to carry out the colouring and format the alignment as Alscript input data was written by Rob Russell and Rich Copley. The columns are calculated by allowing up to 2 invariant positions within each column. The colours correspond to:

Colour	Meaning
Pale blue	hydrophobic
Pale green	conserved polar
Small letters	small residues
Red	fully conserved
Blue text	Proline
Red text	Histidine
Boxed	Aliphatic (L, I or V)
Yellow	Cystine

The 'props' line indicate which residue or property is conserved using the following key:

Character	Property
p	conserved polar
h	conserved hydrophobic
+	conserved positive charge
s	conserved small residues

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