EGCG 8.0
========
Introduction
============
The EGCG package of entensions to the GCG (Wisconsin) sequence analysis
package is now available as a beta release.
A report on EGCG 8.0 is included in the latest issue of embnet.news,
available from the following sources:
URL http://www.sanger.ac.uk/~pmr/egcg.html (EGCG article)
URL http://www.dl.ac.uk/embnet.news/vol2_2/contents.html (vol 2, no. 2)
Throughout the development of the EGCG package, there have been excellent
collaborations with the EMBnet community. Academic software such as EGCG,
developed for a limited number of users, cannot under normal circumstances
be maintained to a sufficient standard for reliable public use. Only the
large number of EMBnet users, and the efforts of the EMBnet support
personnel, have made it possible to produce a robust package. In return, we
receive many suggestions for further developments which we can provide and
test locally and then easily incorporate into the next release.
The EGCG team have fixed the major problems reported by the pre-beta
testers. The beta release should work correctly on Irix 5.2, OSF/1 V3.0,
Solaris 2.3 and OpenVMS-AXP V6.1 systems.
Distribution
============
EGCG is no longer distributed with GCG. We prefer to distribute the
package directly to users through FTP, allowing us to more rapidly
provide new programs and updates, and to keep control of our own
software. The EGCG programs are distributed freely to academic users
throughout the world. The only requirement is that users must have
a valid GCG licence to build the programs.
We have a new E-mail address for support. All questions and comments
about EGCG can now be sent to egcg at embnet.org .
The main distribution site is at The Sanger Centre, Hinxton, UK.
Anonymous FTP: ftp.sanger.ac.uk
directory: pub/pmr/egcg8 (main distribution in .tar.Z format)
directory: pub/pmr/egcg8vms (.bck format for for VMS sites)
The EGCG programs can be installed as a single copy on a mixed unix or VMS
cluster. Separate directories are used for the system-specific files
(object files and image files).
Release Notes
=============
EGCG 8.0 supports GCG release 8.0. The Unix and VMS sources are identical.
Many programs have been significantly improved since the last Unix and
VMS releases of EGCG 7. We are working on full release notes to document
the changes.
Highlights of EGCG 8.0 include:
* All programs now run on Unix and VMS (many were VMS only in EGCG 7).
These include MAPSELECT which creates local enzyme data files;
PEPCOIL which identifies coiled-coil regions and leucine zippers;
NEWFEATURES which analyses and edits the EMBL feature table;
TPROFILESEARCH which compares protein profiles to DNA databases;
and PEPALLWINDOW which plots hydrophobicity for aligned sequences.
* New programs in release 8.0 include POLAND which simulates transition
curves for DNA and RNA; PRETTYBOX which produces shaded sequence
alignments; and STSSEARCH which searches a DNA database for matches
to primer pairs
* The EQuickSearch programs remain fully supported and enhanced in EGCG.
* PRETTYBOX is now an EGCG program.
* Colour options are added to PRETTYPLOT and several other programs.
* Single source version for Unix and VMS to make code management easier.
* EGCG procedure libraries EGENLIB and EGENAPPLIB.
* Standardized user prompts in all programs.
* Full command line control.
* All programs can be run in batch (postponed until GCG 8.1 is released).
* Standardized and simplified graphics routines.
* E-mail support from the EGCG team egcg at embnet.org
Into the Future
===============
Since EGCG was first released with GCG, it has become very popular at a
number of sites around the world. We now have a backlog of program
submissions to include in EGCG which we plan to add as soon as the
C interface to the procedure library is in place. Contributing authors
in the backlog include William Pearson and Rainer Fuchs.
Additional contributions are always welcome.
Acknowledgements
================
We are very grateful to (in alphabetical order) Rein Aasland, Wilhelm
Ansorge, Peer Bork, Thure Etzold, Toby Gibson, Tom Kristensen, David
Mathog, Franc Pattus, Kate Rice, Christian Schwager, Peter Sibbald,
Julie Thompson, Hartmut Voss, Gert Vriend and Rick Westerman for their
many contributions and critical comments as users of the EGCG Programs.
We are also deeply indebted to the staff of GCG Inc. who provided rapid
and helpful answers to our many questions during the development of the
programs. Many thanks to Irv Edelman, Maggie Smith, Donald Katz,
Michael Hogan, Joseph King, Lynn Miller, Mary Schulz and especially
John Devereux.
--
------------------------------------------------------------------------
Peter Rice | Informatics Division
E-mail: pmr at sanger.ac.uk | The Sanger Centre
Tel: (44) 1223 494967 | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919 | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr/ | England
