Using GCG

Getting Started

WB01372_.gif (406 bytes)Initialize the GCG Flat-file Programs
(This is usually done automatically when logging on - You should see the GCG Welcome banner)

analyze% gcgff

WB01372_.gif (406 bytes)Initialize the GCG Relational Database Programs

analyze% gcgrdb
(Provides access to the Oracle-based sequence database)

Help

The GCG manuals are at http://genome.microbio.uab.edu/GCG/GCG10/gcgmanual.html
(Ask Elliot for the username and password)

While on analyze:

WB01372_.gif (406 bytes)genhelp
On-line help arranged by program
WB01372_.gif (406 bytes)genmanual
On-line Manual

Copying Data or Sequence Files

WB01372_.gif (406 bytes)analyze% fetch enzyme.dat
(Restriction enzyme list)
WB01372_.gif (406 bytes)analyze% fetch GE:vsvcg
(The Genbank sequence for vsvcg)

Displaying Data or Sequence Files

WB01372_.gif (406 bytes)analyze% typedata Enzyme.dat
Display the data and documentation
WB01372_.gif (406 bytes)analyze% typedata -ref GE:vsvcg
Display documentation only

Running Programs

WB01372_.gif (406 bytes)Programs

Type the name of the program
Do not abbreviate program names
Program names are case sensitive

WB01372_.gif (406 bytes)Program Parameters

A dash (-) indicates a program parameter
Parameters can be abbreviated
Parameters are case insensitive

Global Switches

Changes your GCG environment
Type at the analyze% prompt
WB01372_.gif (406 bytes)doc
Displays a short paragraph describing the program being run
WB01372_.gif (406 bytes)nodoc
Suppresses the documentation displayed for each GCG program
WB01372_.gif (406 bytes)comcheck
Displays a list of command line options when a program is run
Gives you a chance to enter new options after you have started a program.
WB01372_.gif (406 bytes)nocomcheck
Turns the ComCheck option off.

General Program Switches

Enter on the command line following the program name
Enter at the program prompt if -Check or ComCheck is active
WB01372_.gif (406 bytes) -DEFault
use default values for every parameter not indicated on the command line
WB01372_.gif (406 bytes) -PROtein
sets the program to expect protein sequences.
WB01372_.gif (406 bytes) -NOPROtein
insists that your sequences are nucleic acids.
WB01372_.gif (406 bytes) -CHEck
prints a summary of the available command line parameters

Batch Jobs

Use for programs that may take more than a minute or two to run
Use -Batch to ensure the program will run in batch mode
Use -NOBatch if you do not want to use batch mode
The program will prompt you for required information
The program is automatically submitted to a batch queue

The following programs should be run in batch mode
BLAST
Compare
FastA
FrameAlign
FrameSearch
MFold
ProfileSearch
TFastA

Graphic Output

You must first specify a graphic device before running a program.

WB01372_.gif (406 bytes)analyze% setplot

PostScript Output

WB01372_.gif (406 bytes)Create a PostScript text file

Choose the Postscript option from SetPlot
A postscript graphic file will be created

WB01372_.gif (406 bytes)Create a GIF file
Choose the GIF option from SetPlot
A gif graphic file will be created

WB01372_.gif (406 bytes)Send the PostScript or GIF file to your computer

Use FTP
Be sure to use binary mode for gif files

WB01372_.gif (406 bytes) Edit/Print the GIF or Postscript file

Use Adobe Distiller in the Adobe Acrobat package to create a pdf file from the postscript file
Edit the pdf file using Adobe Illustrator

File Transfer

WB01372_.gif (406 bytes)Use FTP

Fetch (Macintosh); WS_FTP (Windows)

Available from: http://www.dpo.uab.edu/software/ftp/ftpframe.html

Printing

WB01372_.gif (406 bytes)Transfer the file to your computer using FTP and print as you normally would

SeqLab

The Xwindows-based user interface for GCG

WB01372_.gif (406 bytes)analyze% seqlab &

Launches the Xwndows interface for running GCG programs
Must be running an Xwindows package on your Mac or PC

SeqWeb
The Web-based GCG interface
Use a web browser to connect to: http://gcg.genome.uab.edu
Connect using your analyze username and password