 |
The GCG Package |
|
Introduction
The GCG package is a collection of sequence analysis programs which covers most of
the normal requirements of molecular biologists. As the package originated in the
early 80's, it sometimes shows its age. However, recent developments have added
X-windows (SeqLab) and web (SeqWeb) interfaces to the original
command line interface. There is an extensive amount of
documentation for the package which can be accessed via the web.
The three interfaces provided by GCG, and their use are outlined below, as is an
alternative web interface W2H provided by the
EBI.
Command Line Interface
- All the GCG programs can be accessed this way.
- Once you know how, this may be the quickest way to use GCG. Initially it might
seem the most awkward.
- Log in to HKUCC5 (see the startup guide).
- Enter "bruhkstart" to set up the bioinformatics program names.
- Program details by program type or by
program name are available.
- The programs will prompt you for the parameters and files they need or you
can enter the details on the command line.
- Check the programs documentation until you learn the parameters or entering
"program-name -check" will show you the parameters.
- For more details on parameters see
Using Program Parameters.
- To get graphics output you need to set up the
graphics
device (e.g. type "postscript" to produce output suitable for a postscript
printer or ghostview).
- You may need to transfer the graphics file to your PC/MAC by using an FTP program.
- Entering "genhelp" at the prompt will also give you access to the documentation.
- The command line is good for small tasks, when you know your way around the
programs and if you are using a dial-up line.
SeqLab
- SeqLab runs using X-windows and is the easiest way to access most of the GCG
programs (if you can run X).
- Log in to HKUCC5 (see the startup guide).
- Start the X-server on your PC/MAC (see the
X-guide) if you are not on a workstation running X.
- Find the IP address of your PC/MAC (see the
X-guide).
- In your HKUCC5 window set the DISPLAY environment variable to your
PC/MAC/workstation (see the X-guide).
- Enter "bruhkstart" to set up the bioinformatics program names.
- Enter "seqlab" at the HKUCC5 command prompt and the seqlab window will appear.
- Help can be obtained by clicking on the help menu in the SeqLab window.
- Load sequences into the main list or editor or open an existing sequence list.
- From the pull down menus select the programs you wish to run.
- Adjust the parameters by using the options button.
- SeqWeb is GCG's web interface to the GCG package.
- To use it you must get a
SeqWeb account from the computer centre.
- Once you have a SeqWeb account click on the link
Start SeqWeb
either here or on the software page or enter the link
"http:seqweb.hku.hk" in your browser.
- Help for SeqWeb is available at the bottom right of the SeqWeb page.
- The available programs are in the frame on the left and can be ordered
by program group (contents) or by program name (index).
- Only a "core" subset of the GCG programs are available in SeqWeb.
- W2H is an alternative web interface to the GCG package.
- Installation of this interface is not yet complete.
- The documentation for the GCG package is available in several forms.
- For SeqWeb and SeqLab use the help button on the page or main window.
- When using the command line version enter "genhelp" to run the help system.
- Much documentation is also available as web pages.
- Click to access help by:
Last Modified 21/11/01 by
BRUHK support; Copyright © 1999-2001 The University of Hong Kong
This page has been accessed
times.