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HOW TO START GCG
Before you can use the gcg programs, you must activate them, as follows: From the genetics% prompt, type gcg and press enter.
After you type gcg, the gcg banner will appear with a list of databases available. It also tells how to get online help by typing genhelp or using the web. After a moment, the genetics% prompt returns and you can type additional commands. You only need to start gcg once after you login. If you are finished with gcg for the day, you may type exitgcg.
HOW TO RUN GCG
There are several methods for running the GCG programs:
1) Command Line; this is the traditional method with which you type the GCG commands from the genetics% prompt.
2) HYGCGmenu; this is a set of hypertext menus with which you use the arrow-cursor keys to choose programs and select sequences to work with.
3) SeqLab; this is an XWindows based interface with which you use a mouse to select programs, sequences, and databases to work with.
4) SeqWeb; this is a Web-based interface to the GCG Programs.
The first 2 methods can be run from any text-based terminal such as a PC or Mac running NCSA telnet. You can run gcg programs either from the genetics% prompt or from within the HYBROW menu programs by selecting HYGCGmenu from the main menu (you must activate gcg as above before starting hybrow; then start hybrow by typing hy). Experienced users may find it more convenient to run gcg from the command line. However, novice users may find it easier to navigate around in HYGCGmenu, using the arrow keys to select programs and sequence files to work with. These 2 methods work well with either an ethernet connection or a modem connection through the phone lines.
The 3rd method runs GCG through a graphical interface called SeqLab. You open up a set of windows to the GCG programs and use your mouse to make selections, run programs, and view the results. SeqLab has two modes, a main list window and a graphical multiple sequence editor. The graphical multiple sequence editor/alignment window includes a color-coded display of sequence features.
You will need to install an X server program on your PC or Mac in order to use SeqLab. Examples are MacX from Apple and Micro X-Win32 from Starnet. Running XWindows through a modem is possible, but a direct network connection will deliver much better perfomance. Here are the steps for starting SeqLab: 1) Open up an xterm from Genetics to your PC or Mac (read the instructions that came with your X server software); 2) From the genetics% prompt, type gcg, then type seqlab & ; 3) Wait for just a moment until the SeqLab window is opened on your screen; 4) Use your mouse to click on the window buttons to select sequences, or click on the help button for instructions on how to use SeqLab. NB: It is still useful to know how to use GCG commands even with SeqLab.
The fourth method, SeqWeb, allows you to use your Web browser to operate the GCG Programs. Connect your browser to:
http://www.genetics.wayne.edu/gcg/seqweb.html
You need to use Netscape version 4.x or Internet Explorer version 4.x with SeqWeb. The more recent your browser version, the better. SeqWeb has its documentation links from within.
PROGRAM EXECUTION
Most GCG programs execute within a few seconds. The results are often saved in a file in your home directory (or a subdirectory that you have created to contain gcg files). The programs usually offer you a default filename for the output, which you can change if you like before the program executes. N.B. Any already existing file with that same name will be overwritten, so choose carefully.
When you are interacting with the programs, you will often be asked to provide the name of a sequence file or the name of the program on which you want help. From the command line, type the name of the sequence file and press enter. Pressing enter without first typing anything will exit from the program without executing it. This is an easy way to get out of a program that you didn't really want to execute in the first place, or if you want to start over with different parameter values. You can also stop the execution of a program by typing Control-C. If you are using HYGCGmenu, use the up and down arrow keys to point at the sequence file you wish to select and then press the execution key listed at the top of the menu to run the program on that sequence file. If you wish to exit from the menu without running the program, press the left arrow key.
Most of the programs are set to run with certain default conditions that are OK for most people most of the time. You are usually given the opportunity to change some of the parameters before the programs execute. You can also fine tune the manner in which most programs operate by additions to the command line. This can be done both from the genetics% prompt and from within HYGCGmenu, but is entirely optional. Read the Command Line Options section of each program description to learn more about that.
Certain database searching programs in GCG are highly CPU intensive. They have been set up to run in the BATCHMODE, i.e. one search at a time, in the order in which they are received. You do not need to add the -bat switch to the end of the command line. You will receive E-mail informing you when your search is completed, and the results will be written to the file specified at the time the job was submitted. The fastest way to do a similarity search is with NETBLAST, which searches the databases at NCBI directly over the network.
HOW TO LEARN ABOUT GCG
All the program manuals and documentation are available on our Web site at http://www.genetics.wayne.edu/dwomble/gcghelp.html The documentation is available in both HTML and PDF format. You can read or print the manual sections for your own use. If you wish, you may purchase printed copies of the official manuals, including nice official binders, from GCG for about $200 (contact beers@gcg.com).
The manuals are also available within GCG by typing genmanual or genhelp (after first activating gcg as described above). The Users Guide offers general information about UNIX commands and the gcg system; please read the section entitled Getting Started for an introduction to GCG and to simple, useful UNIX commands. The Program Manual offers complete descriptions about each program in the package. Each description includes an example of how to use the program. The SeqLab Guide explains how to use the XWindows interface with the GCG programs.
You may print PostScript sections of the online manual for your own use. To do that, use the GCG Red command and save the output to a PostScript file (read the file gcggraphics for instructions on how to do this). Then, use ftp to transfer the files to a PC or Mac attached to a PostScript printer such as an Apple LaserWriter or an HP LaserJet 4M, and send the files to the printer.
The manual within GCG uses the text WWW browser LYNX to display the manual sections. To see all the text as well as images, use a browser such as Netscape or Internet Explorer from your PC or Mac to view the manual.
Help for individual topics is also available on the menu screens in HYGCGmenu. Instructions for setting up your graphics environment, so that you can print graphs such as RNA or protein secondary structure predictions, are located on the Display / Graphics menu in HYGCGmenu (select Help).
Please try browsing through the manuals to learn a little about what gcg can do. GCG also publishes a newsletter (for a free subscription, send a request to newsletter@gcg.com). There is a section of the USENET News devoted to using GCG. Use a newsreader program to subscribe to bionet.software.gcg.
DISPLAYING AND PRINTING GCG GRAPHICS AND OTHER FILES
Many programs in GCG have graphic output, such as restriction maps or RNA secondary structure predictions. You have several choices as to how to handle the graphic output: 1) display it on your screen; 2) print it directly to the printer attached to your PC or Mac terminal; 3) save the output to a file and then print it later. Please read the file gcggraphics for detailed instructions on how to display or print the graphics and other files.
GCG WORLD WIDE WEB HOME PAGE
Please visit the GCG home page on the World Wide Web at:
You can use Netscape or Internet Explorer on your PC or Mac, or Lynx on Genetics. There is information about the GCG programs, their newsletter, the usenet group bionet.software.gcg, and complete sets of hypertext GCG manuals that you can read, save, or print. There are also links to other WWW sites of interest to molecular biologists.
WHAT PROGRAMS ARE AVAILABLE WITH GCG
Here is a list of general categories of programs available in GCG:
Editing Sequences Fragment Assembly Restriction Mapping Sequence Comparison Database Searching / Retrieval Multiple Sequence Analysis DNA Sequence Pattern Recognition RNA Secondary Structure Protein Sequence Analysis Translation Manipulation Display / Graphics Convert Sequence Format File Management UtilitiesBIOPORTAL
BioPortal provides an experimental user-friendly World Wide Web (WWW) interface to the GCG programs and other biosoftware running on the Genetics computer. The Genetics BioPortal interface is available at: http://cmb.biosci.wayne.edu:8888/
BioPortal is available only to WSU scientists who have registered login accounts on the Genetics computer.
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Copyright © 1997 - 2002, David D. Womble.