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The package can be obtained from the Genetics Computer Group, 3575 Science Drive, Madison, WI 53711, (608) 231-5200, Fax: (608) 231-5202, e-mail:, URL. The programs are generally run from the C shell in the UNIX environment. It is suggested that a minimum of 128 megabytes of core memory be provided with 200 megabytes of virtual memory. Additional disk space for individual usersвЂ™ files is also needed. The disk space requirement is increasing rapidly with the expansion of the databases.

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A minimum of 15 gigabytes of hard disk space is needed to install and maintain the Wisconsin Package with its entire set of databases. The package will also run on a Digital Alpha machine running OpenVMS versions 6.2 or 7.1. The package can be installed on several different kinds of computers, including Digital Alpha machines running Digital UNIX 4.0, Silicon Graphics RISC-based machines running IRIX versions 6.2, 6.3, or 6.4, and Sun SPARC-based machines running Solaris versions 2.51 or 2.6. Materials The methods described here are for the GCG program package version 9.1, installed on a shared computer with a UNIX operating system connected to a TCP/IP network (2).

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It is possible to print additional copies of most of the manuals from within the GCG programs if that is desired.

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A system support manual describes how to install and maintain the Wisconsin Package and its databases. A userвЂ™s guide provides a complete introduction to all of the general features of the Wisconsin Package, including helpful information about useful, simple UNIX commands that will help one manage GCG sequence files. The program manuals provide complete descriptions of all the programs, including examples of how to use each one. Also included are complete sets of user manuals, in both printed and online Web-based versions. The sequences in the databases are suitable for direct submission into the GCG programs for analysis, manipulation, or comparison.

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The complete GCG package also includes a full set of nucleic acid and protein sequence databases.

Web-based interfaces for GCG are described in Chapter 2.

A recently introduced Web-based interface, called SeqWeb, is also available from the GCG and allows users to run GCG programs and manipulate sequence files through a Web browser such as Netscape Communicator or Internet Explorer. In the authorвЂ™s experience, students who are newly introduced to the GCG programs often prefer the easy-to-use SeqLab graphical interface, whereas experienced GCG users often prefer the command line, because it is inherently faster, especially over a network from a remote workstation. Gram in the suite, all the other programs will operate in a similar fashion. 132: Bioinformatics Methods and Protocols Edited by: S. Once an individual is familiar with how to run any given proFrom: Methods in Molecular Biology, vol. With either interface, all programs operate similarly to each other. SeqLab also includes a powerful color-coded graphical multiple sequence editor.

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Two methods included with the package are the command line interface, which is the traditional method in which users type the name of a GCG program to initiate an interactive program session, and a graphical user interface (GUI) called SeqLab, in which users open a set of windows to the GCG programs and interact graphically to select sequences and program functions. There are several different methods for operating the GCG programs. The Wisconsin Package is installed commonly on a shared computer on a network, such as a UNIX server, so that individuals may access the programs and use them from remote locations, such as from their own personal computers (PCs) or other kinds of terminals. In many cases, complex problems can be solved by using several GCG programs in succession. The output files from many GCG programs are suitable as input to other GCG (or other) programs. Most GCG programs use one file as input and write the results to another file. The Wisconsin Package includes more than 130 programs, each of which functions as a tool for performing a specific task, such as translating a nucleotide coding sequence or determining restriction enzyme cutting sites. The initials GCG stand for Genetics Computer Group, which is a subsidiary of Oxford Molecular Group (Campbell, CA). Introduction The GCG programs, also called the вЂњWisconsin Package,вЂќ comprise a powerful suite of tools for manipulating, analyzing, and comparing nucleotide and protein sequences (1). Bioinformatics Methods and Protocols Edited byДЎ GCG: The Wisconsin Package of Sequence Analysis Programs David D.