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[ANNOUNCE] Jpred2 - secondary structure prediction

James Cuff james at ebi.ac.uk
Thu Nov 11 07:09:50 EST 1999

                   /* Announcing Jpred2 (alpha) */

The Jpred prediction service has been extended.  Jpred2 includes the
following additional features:

- Jnet, a consensus neural network secondary structure prediction method,
  which includes solvent accessibility predictions

- DSC 1.2 predictions.  DSC 1.2 contains an updated and more accurate 
  GOR matrix, which was found by the authors of DSC to improve prediction 
  accuracy by 0.5 to 1%.

- Jpred2 applies a 3 iteration PSI-Blast search to obtain sequences, and
  construct a multiple sequence alignment for secondary structure prediction. 

- A filtered sequence database is used to search for related proteins 
  to the query sequence.  The filtering masks out any low complexity, 
  transmembrane, or coiled coil regions. The software for filtering 
  the database was written and kindly supplied by Dr. David Jones.
- Jpred now predicts coiled coil regions with both COILS (Lupas, A., 
  Van Dyke, M., and Stock, J. (1991), Science 252 1162-1164), and 
  MULTICOIL (Wolf E., Kim P. S, Berger B., (1997) Prot. Sci. 6 1178-1189)

- PHD transmembrane helix predictions are also included.

- A parallel version of CLUSTALW from SGI is applied, to speed up the 
  multiple sequence alignment building process.

- The Jnet algorithm now forms the default prediction method, 
  making for faster and more accurate predictions.  However, the other
  prediction methods are still available.

- See the Jpred2 web pages for further information and references.

- Availability:

  The Jpred2 homepage can be accessed from the old Jpred pages at:

  http://circinus.ebi.ac.uk:8081/  and from the new Jpred2 pages at:


  Jpred2 may also be reached from the software pages of the Barton 
  group web server at the EBI:


  Both Jpred and Jpred2 will run together until futher notice. 
  Eventually the original Jpred server will be retired.

Best regards,


          James Cuff          |  European Bioinformatics Institute
     +44 (0) 1223 49 4607     |     Wellcome Trust Genome Campus
 http://www.ebi.ac.uk/~james  |   Hinxton, Cambridge. CB10 1SD, UK

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