Jpred
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Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server[1] which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction,[2] that has existed since 1998 in different versions.[3]
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.[4]
JPred 2
The static HTML pages of JPred 2 are still available for reference.[5]
JPred 3
The JPred v3[6] followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References[7]). 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%.[2]
- 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.[8]
- Added prediction jobs monitoring tools.[9]
- 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.[10]
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.[11]
See also
References
- ↑ "JPred4: A Protein Secondary Structure Prediction Server". http://www.compbio.dundee.ac.uk/jpred4/. Retrieved 16 July 2015.
- ↑ 2.0 2.1 Drozdetskiy, Alexey; Cole, Chris; Procter, James; Barton, Geoffrey (Apr 16, 2015). "JPred4: a protein secondary structure prediction server". Nucleic Acids Research 43 (W1): W389–W394. doi:10.1093/nar/gkv332. PMID 25883141.
- ↑ "JPred old news". Oct 25, 1998. http://www.compbio.dundee.ac.uk/jpred4/old_news.shtml. Retrieved 16 Jul 2015.
- ↑ "JPred4 statistics". http://www.compbio.dundee.ac.uk/jpred4/stats.shtml. Retrieved 16 July 2015.
- ↑ "JPred2: legacy". http://www.compbio.dundee.ac.uk/jpred4/legacy/. Retrieved 16 July 2015.
- ↑ "JPred3: previous version of JPred". http://www.compbio.dundee.ac.uk/jpred3/index.html. Retrieved 16 July 2015.
- ↑ "JPred4 references". http://www.compbio.dundee.ac.uk/jpred/refs.shtml. Retrieved 16 July 2015.
- ↑ "JPred4 RESTful API". http://www.compbio.dundee.ac.uk/jpred4/api.shtml. Retrieved 16 July 2015.
- ↑ "JPred4 monitoring tools". http://www.compbio.dundee.ac.uk/jpred4/monitor.shtml. Retrieved 16 July 2015.
- ↑ "JPred4 Help and Tutorials". http://www.compbio.dundee.ac.uk/jpred4/help.shtml. Retrieved 16 July 2015.
- ↑ Cuff, JA; Barton, GJ (August 2000). "Application of multiple sequence alignment profiles to improve protein secondary structure prediction". Proteins 40 (3): 502–11. doi:10.1002/1097-0134(20000815)40:3<502::aid-prot170>3.0.co;2-q. PMID 10861942.
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