PLEX Announcements

Current version: v2.4
Release date: Sep 22 15:59 CST 2004
Report bugs to: marcotte at icmb dot utexas dot edu
[ Announcements in red indicate major changes ]

We had to shut down PLEX on Dec 10, 2004, due to server problems. Unfortunately, someone tried to mine PLEX using a script. We request our users to refrain from using such autosubmit scripts. If you are interested in data, please write to us, and we may just give it to you!! Meanwhile, if you still experience problems, do let us know.
Thanks!
- The PLEX Team
Bug fixes
- Links to old html pages were causing problems [Fixed|svd|9/25/04]
- Name tags missing (for 'I have a Genbank identifier' etc.) [Fixed|svd|9/25/04]
Notes
- Text files (and some other files as well) created in a windows environment tend to retain a '^M' character at their line breaks. If you notice anything funny happening with your output, maybe its windows!

- The tale of the missing GIs: If you happen to input a Genbank identifier that does not bring up a sequence, or your desired sequence, our version of the non-redundant database (nrdb) is older than the one you referred to. Please use the amino acid sequence directly, in such instances.
Version announcements

September 24, 2004:
  • Input interface changed
September 22, 2004:
  • PLEX version 2.4 live!!
  • Database can now be searched based on operator and Evalue inputs alone, and a precreated profile can be pasted in directly
February 22, 2004:
  • PLEX version 2.2 live!!
  • Profile resolution script now gives more information
  • Few old bugs fixed
  • Completed new help file
  • Sequences can now be input without a comment sign ('>')

Version 2.0

January 21, 2004:
  • Extensive modifications to the following scripts over the month of December and January:
    - Script for comparing phylogenetic profiles [ code changes for display ]
    - Script for drawing profiles [ code changes for display, speed ]
    - Script for displaying Rosetta stone protein links [ new code ]
    - Script for finding gene neighbors [ new code ]
November 3, 2003:
  • Rosetta stone datasets created for all euks except humans in our database [ see list ]. These are accessible via PLEX.
October 23, 2003:
  • Rosetta stone datasets created for all bacterial and archaeal genomes in our database [ see list ]. These are accessible via PLEX.
May 28, 2003:
  • 'Vibrio cholerae - Whole genome' search option removed from phylo-profile-comparison Users will not be able to compare phylogenetic profiles against the whole Vibrio genome. There seems to be a problem with the database searching for Vibrio.
  • Program for drawing profiles modified, so the initial query is not redrawn after an iteration (and thus avoiding confusion!).
  • Help file moved to the correct location.
May 27, 2003:
  • 'Gene neighbor' finding service now fully functional and available from within PLEX.
May 22, 2003:
  • 'Finding gene neighbours' feature added to the 'analyze selection further' section.
Feb (over the whole month):
  • PLEX moved to the new apropos server.
  • Compare against 'all genomes' option removed, is too computationally expensive for the current server
Announcements prior to Feb 2003 are available on request. Announcements for previous versions are not maintained.
 Copyright notice: Copyright © 2002 - 2005, Shailesh Date and Edward Marcotte. The protein link explorer data and server is the property of the University of Texas, and cannot be used for commercial purposes without written permission of Edward Marcotte and the University of Texas. It is forbidden to redistribute, derivatize, or encapsulate the protein link explorer data or server in another database without permission. Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of the University of Texas and Edward Marcotte. All copies or mirrors of the protein link explorer must carry this notice.