Frequently Asked Questions

What is Jpred?

Jpred is a web server that takes a protein sequence or multiple alignment of protein sequences, and from these predicts secondary structure using a neural network called Jnet. The prediction is the definition of each amino acid residue into either alpha helix ('H'), beta sheet ('E') or random coil ('-') secondary structures.

Jnet also makes predictions of relative solvent accessibility. Using the 0%, 5% and 25% cut-offs Jnet predicts whether a residue is burried ('B') or exposed ('-') at each of the three relative solvent accessibilities.

Additionally, Jpred makes coiled-coil predictions using the 'COILS' alogithm developed by Lupas and co-workers.

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 format or BLC format, and the predictions will run. 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.
What do I need to run Jpred?

The Jpred webserver has been written in standards compliant XHTML 1.0 and CSS 2.0 and will work with any current browser that supports these standards. It has been tested with Firefox (Linux, Windows and OS X) and Internet Explorer (versions 6 and 7). If you wish to use Jalview you will need a browser that supports Java 1.1, this includes most modern browsers.

Can I still use Jpred 2?

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

Are there any example files?

Yes. For the Raw, MSF and BLC inputs.

How long do I have to wait?

That's 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 an hour. According to our statistics ~98% of submissions complete within an hour, and of those, >90% complete within seven minutes.

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 an hour.

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

Sorry. The source is in no state to be released due to general ickyness. However, we may get round to making the source less horrific and releasing it. Drop us a line and if enough people request a release we will consider it.

What are all the output files?

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

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

The viewer and editor, Jalview was originally written by Michele Clamp and development has continued with Andrew Waterhouse, Jim Proctor and David Martin. The source code and the program is available for download.

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. All jobs are removed from the server after two days, however, in order to monitor the server, we maintain statistics on the use of the server.

Are there any known bugs?

When pasting sequences into the search make sure that their are no extra characters or comment lines as these will cause Jpred to fail. When using your own multiple sequence alignments it is highly recommended to upload the file rather than pasting as problems in the formating can occur.

If you see any other strange behaviour don't hesitate to contact us, and we'll try our best to repair or explain the problem.

Where did Jpred come from?

The server is 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%.

What are 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.

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