GCG

General

The Wisconsin Package GCG is a software suite that contains over 130 sequence analysis tools. It was developed by the Genetics Computer Group in Madison and is now maintained and distributed by Accelrys. It can be accessed remotely from any networked computer. There are three different interfaces for accessing GCG:

Command-Line
SeqLab: graphical X-windows interface
SeqWeb: web browser interface (http://gcg.ucr.edu)

All three applications are installed at UCR on the UNIX server cache.ucr.edu where they share the same sequence databases.

Requirements

Command-Line and SeqLab

In order to use Command-Line GCG and SeqLab, you need to set up an account on cache.ucr.edu by emailing Terri McDonald (terri.mcdonald@ucr.edu) your user name and password. To run SeqLab from a PC, you need to open X-Win32 first and then connect from the PuTTY terminal via ssh (configuration). For Mac OS X we recommend using the new X11 terminal (configuration). The instructions on the environment settings for older MAC systems can be found on http://kansas.ucr.edu/exodus/. For an efficient file exchange between UNIX and your local computer, we recommend using WinSCP for PCs and fugu for Macs.

SeqWeb

To get an account for SeqWeb, please email Brad Hyman (bhyman@ucrac1.ucr.edu) your user name and password. After your account is active you can access SeqWeb by sending your browser to http://gcg.ucr.edu and typing in your user name and password in the login window.

Command-Line

The basic Command-Line interface provides access to all ~130 GCG programs, which are started from an X terminal like PuTTY (PC) or X11 (Mac OS X). Its scriptability allows repetitive analyses.

To start GCG from your X terminal application (see above), type the following command:

$ gcg

SeqLab

SeqLab is a point-and-click X Windows interface to almost all GCG programs. Its centralized main window and UNIX based file management facilitates numerous tasks at once.

To start SeqLab from your X terminal application, do the following:

From a PC start X-Win 32 first. Then type:
$ seqlab &

SeqWeb

SeqWeb is a point-and-click browser interface to a subset of GCG programs. To start it, send your browser to http://gcg.ucr.edu, then provide your user name and password in the login window. Instructions on how to set up a SeqWeb account can be found above.

More Help

Help on using the different GCG programs can be found within each application, in the UCR SeqLab Manual or on the Accelrys help page.

Maintained by Thomas Girke. Last Modified: Thu, March 27, 2003