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Tools for post-processing PredictProtein results

PredictProtein usually displays alignments and predictions in a very simple ASCII format. You can obtain some more 'fancy' alignment views using one (or many) of the following methods for post-processing the results you obtained from PP.


Display of alignment and predictions
ACTION HTML version of results
Tool PredictProtein
Description The display of PredictProtein in HTML (viewable for your WWW browser, e.g. Netscape) is an option you can select when submitting your request. At this point, we do NOT offer a conversion of PP results to HTML, rather we suggest you resubmit your request with the appropriate choices.
Note: PP results in HTML can become very large, you may want to check the box 'Results on FTP site, NOT in email' to not let your email overflow.
ACTION Postscript, TIF, or GIF images of results
Tool ESPript
Authors Patrice Gouet and Emmanuel Courcelle
Please quote P Gouet, E Courcelle, D I Stuart & F Metoz: ESPript: multiple sequence alignments in PostScript. Bioinformatics, 15, 305-308, 1999.
Description ESPript converts the PredictProtein results (and other alignments) into fancy images.
To use the tool, you have to do the following:
  1. Save the PredictProtein results into a file.
  2. Load ESPript (see below)
  3. Provide the file in which you saved the results in the appropriate boxes of ESPript (click 'Browse ..' boxes in upper half)
  4. Run ESPript (click 'Run ESPript' button on lower left corner)
Go to ESPript local mirror in New York: http://cubic.bioc.columbia.edu/cgi/pp/ESPript
original ESPript site in Toulouse: http://www-pgm1.ipbs.fr:8080/ESPript/



Display of PHD results
ACTION Map PHD predictions onto similar structures (if found)
Tool scop
Authors Alexey Murzin, Bartlett Ailey, Steven Brenner, Tim Hubbard, Cyrus Chothia, (contact: scop@mrc-lmb.ac.uk)
Description If you suspect that a protein of known structure is similar to the protein you submitted to PredictProtein, then you can map the PHD prediction onto that structure. Simply take the PHD prediction out of the results and paste it into the appropriate box.
Note: this is for experts, only. You must have a reasonable first guess about a similar protein structure, and must locate that structure in scop.
Go to scop http://scop.mrc-lmb.cam.ac.uk/scop/



General alignment display tool
ACTION Display and edit alignment (JAVA alignment viewer)
Tool Jalview
Authors Michele Clamp
Description Jalview is a JAVA alignment viewer, and editor.
The program may crash once in a while, but its features are purely outstanding!
Go to Jalview http://circinus.ebi.ac.uk:6543/jalview/

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