GCG Wisconsin Package

Description

The GCG Wisconsin Package is an integrated package featuring a comprehesive collection of DNA-, RNA-, and protein-sequence-analysis tools. It integrates many software such as recent the MEME/MAST suite of de novo pattern-discovery programs, the Staden sequence-analysis package, the HMMER Markov-model construction suite, and the PFAM protein-motif database.

Two user interfaces, Command Line and SeqLab are currently provided.

This package provides access to over 130 programs. The major functions of GCG include:

• Comparison
• Database Searching and Retrieval
• DNA/RNA Secondary Structure
• Editing and Publication
• Evolution
• Fragment Assembly
• Gene Finding and Pattern Recognition
• Importing and Exporting
• Mapping
• Primer Selection
• Protein Analysis
• Translation

Home Page

http://www.accelrys.com/products/gcg_wisconsin_package/index.html

Available Databases for GCG

The available databases, release number, and release date for GCG Wisconsin Package will be displayed when you initiate your GCG working environment by typing in gcg command at the prompt. More information can be found at the GCG Database Tables

Tutorial

The SeqLab Tutorial book from GCG is available at bscl:

Documentation

These User Guides from GCG are available at bscl:

• Program Manual (volume 1)
• Program Manual (volume 2)
• User's Guide UNIX
• Command-Line Summary
• SeqLab Guide
• SeqLab Tutorial
• Training Course

More information can be accessed by typing in genhelp or genmanual on UNIX terminal.

Online documentation can be found for GCG Help, GCG Manual, and User's Guide (access is allowed only to University of Minnesota Network).

Running GCG programs

To use gcg, login into cgls1.msi.umn.edu or bi7.msi.umn.edu using ssh. You then call gcgstartup script to define key GCG environment variables and "gcg" alias by typing:

source /usr/local/gcg/gcgstartup

Or put these lines into .cshrc file at your home directory

if ( -e /usr/local/gcg/gcgstartup ) then
  source /usr/local/gcg/gcgstartup
endif

Then type:

gcg

to initialize GCG working environment. You will see a brief information about GCG Wisconsin Package and available databases. Then you are ready to use any of program in GCG package.

To use GCG X-window interface SeqLab, on UNIX terminal, type in

seqlab &

Version: 10.2 and 10.3
Labs: Basic Sciences Computing Lab, Computational Genetics Laboratory
System(s): SGI workstation (bi7) and SUN (cgls1)
Categories: Bioinformatics