A Protein Secondary Structure Prediction Server

JPred News

10 Aug 2015
  • We reviewed and expanded level of details we provide about JPred/JNet ANN training (corresponding to the current JNet v.2.3.1). Details are linked from About page from under "Data" section. Following is the direct link to details/downloads, and summary tables: link.
7 Aug 2015
  • JPred has now reduced output: we decided to retire HTML files with full MSA-s for sequence based jobs (and we used this occasion to also get rid of bulky *.ps files, while keeping *.pdf-s, as well as HTML and SVG visualizations of results). The full alignemnts (with all gaps and insertions) are still available in FASTA format as part of JPred results and through Jalview. Note that Jalview since some time now has the ability to display and work with full alignments (with gaps and insertions reported from JPred) and that was the reason to retire static HTML copies of the MSA-s. As before - links to launch Jalview applet or full application - are available for every job.
10-14 Jul 2015 (+ 24 Jul 2015)
3 Jul 2015
  • JPred has now an extension added: checking if results for a query sequence exist in JPred cache and if they do - retrieve those instead of starting a new job and re-creating the same results. We performed test of the new functionality, but may have missed something. For example, not all "temporary" files are cached. If you see your favorite files missing or any other issue - please let us know: contact us. (NOTE: if results are retrieved from the cache, in the results directory you will see "README_more_details" file.)
1 Jul 2015
  • Updated daily/monthly overall JPred jobs statistics plots, see: link. We hit a new record in the number of JPred jobs run in one months: 138,090 jobs (!) in the month of June'15.
17 May 2015
  • JPred4 got a well deserved speed up. The JPred execution time per job improved by up to a factor of 10!! So, jobs which were taking 10-20min before will take about 1-2min now. (The improvement is not linear - jobs which were taking a long time before e.g. hours, would still take a while, but those kind of jobs are rare.) This means faster delivery of the results and more jobs served. Enjoy!
14 May 2015
  • We added a mass submission, status check, and results retrieval script. Whether you would like to submit 1, 100, 100,000 JPred jobs - this is probably the most efficient and easiest way to do it (virtually with "a push of a button". Details are here: link (look for the option number 1). Give it a try!
8 May 2015
1 May 2015
  • JPred4 is now the "default" version of the JPred server. In case one still would like to use JPred3, it is available through the following link. Please note however that the JNet (prediction engine behind JPred) is the same (and upgraded since 19th Aug 2014) for both JPred3 and JPred4 and JPred4 has multiple interface improvements and added tools like REST API and Monitoring as well as improved batch submission and results reporting for batch mode. As always, if you have any questions - please don't hesitate to contact us.
16 Apr 2015
  • JPred4 paper is published: Drozdetskiy A, Cole C, Procter J & Barton GJ. (first published online April 16, 2015) JPred4: a protein secondary structure prediction server, Nucleic Acids Res. Web Server issue [doi:10.1093/nar/gkv332]
27 Mar 2015
  • JPred jobs monitoring is now available. With real-time updates of JPread server/cluster load one can predict dynamics of jobs submission/running and possible waiting time. For full details see the following page.
04 Mar 2015
  • 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.
22 Dec 2014
  • JPred server is upgraded to v.4.0.0. JPred 4 incorporates JNet v.2.3.1 as announced earlier (see the news item for 19th Aug 2014). The updated JNet since then was tested by over 41,500 successfull jobs. For JPred 4 we also updated the web-site/interface to utilize the latest technologies improving the design and usability. We also advanced results reporting, as well as incorporated tool-tips, and added step-by-step easy to follow tutorials.
  • We plan to Run JPred 4 for about a month at http://www.compbio.dundee.ac.uk/jpred4 alongside the current JPred 3 at http://www.compbio.dundee.ac.uk/jpred. Later, around end of 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 a smooth transition. Starting January 2015 all upgrades will be performed on JPred 4.
19 Aug 2014
  • JNet (now v.2.3.1) was re-trained using most up-to-date SCOPe 2.04 data and UniRef90 release 2014_07, 09-Jul-2014. Using both PSIBLAST and HMM accuracy will average 82.0%.
03 May 2013
  • Due to continued, systematic abuse of the batch system by a user we have been forced to severely limit batch jobs to one hundred per day per user.
02 May 2013
  • Owing to excessive usage of JPred over the last few days, we have had to reduce the daily job submission limit to 1000 from 4000. We will review this when things have calmed down.
29 April 2013
  • An upgrade to our cluster systems has been successfully implemented and JPred is back up and running. If there are any problems please let us know via the usual methods.
29 May 2012
  • Last week JPred went down to a problem with the filesystem. It is back up now, but will be running with reduced resources so batch submissions will be limited until we're back to full strength.
06 April 2012
  • We had a serious issue with our job queuing system last night and this morning, which resulted in all jobs submitted during this time failing. The issue has been fixed, but unfortunately all failed submissions were lost. You'll need to re-submit any failed jobs. Apologies.
28 June 2011
  • Owing to excessively large submissions to JPred over the last few months, we have set a maximum limit of 4,000 predictions per user per day. This is to avoid JPred being swamped given the resources available. If this limit is not sufficient for your needs, please contact us and we will happily discuss your requirements.
22 June 2011
  • It looks like JPred was too popular for its own good over the last couple of days and ran out of space, again. More space has been made available and JPred is running normally, now.
02 May 2011
  • Over the last couple of days JPred has received over 20,000 job submssions causing it to run out of disk quota. Thus, any subsequent submissions will have failed.
    Space has been cleared and JPred is working normally again. We are very heartened that JPred is still of great use to the community, but can we request that if you do want to submit large numbers of searches to please spread them over several days. Thank you.
07 October 2010
  • Last night JPred used up its allocated quota of disk space and stopped working. Space has been cleared and the quota adjusted so hopefully this is unlikely to happen again. JPred is working as normal now. Apologies for any inconvenience.
17 February 2010
  • JPred is now back following the essential maintenance. All should be back to normal. Please let us know of any problems.
04 February 2010
  • Update. Unfortunately, the maintenance has had to be postponed. We'll keep you posted.
01 February 2010
  • Advanced Notice On 3rd Feb. JPred will be going offline from approx. 17:00 GMT and will be back approx. 09:00 GMT the day after. This is due to essential maintenance. No JPred jobs will be accepted or run during this time.
10 December 2009
  • JPred jobs have been restricted at the moment while we resolve a problem with our systems. Jobs will run, but they will take longer than usual. Please bare with us while we get things back to normal.
14 September 2009
  • Unfortunately, we had a problem with the submission of jobs over the weekend. Some jobs failed, but the majority were queued up. It has now been fixed and JPred is working through the backlog.
25 August 2009
  • A recent change to JPred temporarily broke JPred predictions from MSA files. This was fixed today and all is working as normal. Apologies for any problems caused.
13 August 2009
  • Following the release of SCOP 1.75, Jnet has been retrained and updated to version 2.2. Concurrently, the UniRef90 sequences have been updated to release 15.4. On a blind set of 150 sequences Q3 accuracy has been determined to be 81.6%
30 September 2008
  • JPred 3 is back up after a successful migration. JPred should be working as before, only faster. Please report any problems
22 September 2008
  • UPDATE: The JPred migration will happen between 26th and 30th September, inclusive. During this period JPred should be considered unavailable even if the site appears to be working. There will be no change in functionality, but it will have access to a much larger cluster thereby increasing throughput.
09 September 2008
  • We will soon be making a significant migration of the JPred service to a new server. During this time the server will be unavailable and any stored results should be considered lost. It is likely to take several days to complete the migration and perform tests to ensure consistency of service. More information will be posted nearer the time.
04 August 2008
  • In order to allow interactive jobs to run more promptly, batch jobs are now run at a lower priority. This is unlikely to make a big difference in the time it takes to run batch jobs, but interactive jobs will spend less time waiting to run.
5 June 2008
  • Yesterday (04 June 2008) we had a disk failure which caused an instability in our filesystem for JPred jobs. As such some (not all) files written will have been corrupted. Unfortunately, it is difficult to tell exactly which, therefore it is recommended that any jobs run on 4th June be re-run as a precaution. Sorry for the inconvenience.
8 May 2008
  • A paper describing JPred 3 has been published in Nucleic Acids Research Advanced Access
15 April 2008
  • JPred was down briefly today due to the server running out of disk space. Some jobs over-night also failed because of this. The issue has been resolved and normal service has been resumed.
  • In addition, over the last couple of weeks, a few jobs have failed. It seems to have been caused by failures in writing temporary files, but it was difficult to reproduce. We have implemented a fix and will be monitoring the situation.
2 April 2008
  • Alignments and single sequences are now accepted in Fasta format. The 'Advanced' page has been modified to accommodate this change.
  • The prediction and alignment ouputs are now available in Fasta format as well. See the .concise.fasta file in the raw output.
  • An odd bug where uploaded single files which had hits to the PDB failing to 'continue' has been fixed.
23 January 2008
  • MSF/BLC alignment inputs can now have lower-case residue codes in their sequences.
18 January 2008
  • Update The problem has been fixed and everything should be back to normal.
  • We are currently having problems with sending emails. The feature has been disabled until it is resolved. Interactive jobs are working as normal.
7 January 2008
  • JPred 2 (the old version) had an unexpected server problem on New Year's eve, which meant that no JPred (2 or 3) jobs were run until the 2nd January. The issue has been resolved, but means that JPred 2 will be switched off sooner rather than later.
18 December 2007
  • JPred 3 is now the default version and fully functioning!
  • Now with added batch job goodness
10 December 2007
  • Jobs which 'Timeout' now correctly inform the user of the fact on the 'Results' page and by email (if provided).
21 September 2007
  • Adding new functionality to the Jalview applet to be able to run full the application. See under the 'File' menu in the applet.
  • The links to PDBsum on the 'Matches to PDB' page now open in a new window.
  • An obscure bug in the rendering of PS/PDF outputs has been fixed.
21 August 2007
  • The JPred server was down this morning for a few hours due to unscheduled downtime of the servers.
09 August 2007
  • JPred server version 3 is released as a beta to run in parallel with version 2. Many improvements and bug-fixes have been implemented.

Old News

Primary citation: Drozdetskiy A, Cole C, Procter J & Barton GJ. Nucl. Acids Res.
(first published online April 16, 2015) doi: 10.1093/nar/gkv332 [link]
More citations: link.