Before You Begin

[ Program Manual | User's Guide | Data Files | Databases ]

Table of Contents

About the Wisconsin Package...

Using This Manual

Conventions Used in this Guide

How This Guide is Organized

Getting Help

Using Online Help

Using GCG Technical Support

Getting Wisconsin Package Training

Using Companion Documentation

Ordering Additional Documentation

Photocopying or Printing Documentation

About the Wisconsin Package...

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The Wisconsin Package^(TM) is an integrated package of over 130 programs that allows you to manipulate and analyze nucleotide and protein sequences. Scientists from all over the world have collaborated to develop and refine the Wisconsin Package, making it a flexible tool with which to analyze your sequence data.

Among its many features, the Wisconsin Package lets you

• Enter sequences from a digitizer or a keyboard and edit them.

• Manage and assemble nucleotide sequence fragments in a sequencing project.

• Calculate and display restriction digests and simulate RNA fingerprints.

• Compare sequences.

• Search nucleic acid or protein sequence databases for sequences similar to your query sequence or sequence pattern.

• Create, edit, display, and analyze multiple sequence alignments.

• Determine and display evolutionary phylogenies from multiple sequence alignments.

• Recognize terminators, repeats, protein coding regions, and other consensus patterns.

• Predict and display optimal and suboptimal RNA secondary structures.

• Identify sequence motifs in protein sequences and make predictions about peptide isolation.

• Translate nucleic acids into proteins and backtranslate proteins into nucleic acids.

• Predict optimal primers for PCR reactions.

Using This Manual

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This User's Guide provides information about Wisconsin Package commands and concepts. It is designed to be both a beginner's guide to working with Wisconsin Package programs and an intermediate and advanced user's reference to general concepts that all the programs use as their foundation. This guide can serve as an introduction to the Package or as a tool to enhance existing skills.

You do not have to read this manual front-to-back. It is designed around common tasks that you will perform, with headings and subheadings that allow you to scan the pages easily and zoom in on the information you are interested in. Take some time to browse through these tasks. You may discover things that will make your work with the Package more efficient and effective.

Conventions Used in this Guide

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Some conventions in this guide make the text easier to read. Becoming familiar with these conventions will help you extract the information you're interested in.

TIP - This symbol indicates a helpful hint which might make your work easier.

Text Conventions

A special typeface (Courier, also known as typewriter font) indicates characters you should type. For example, consider the following command line:

% mapsort [-INfile=]ggammacod.seq -BEGin=93 -END=315 -Default

• Many parameters have a value. For a few of these parameters you have the option to omit the qualifier (for example [-INfile=]) and simply type the value (for example ggammacod.seq). Square brackets [ ] surrounding a qualifier indicate that typing it is optional. Such a parameter is called an unqualified parameter. For instance
  
  % map -INfile=ggammacod.seq -Default
  
  is the same as
  
  % map ggammacod.seq -Default

  Note: Do not type the square brackets [ ].

• To invoke command-line parameters, bold uppercase text indicates the minimum number of letters you must type (for example -BEGin=93). That is, some parameters can be abbreviated (-BEG=93). You can type more letters than those indicated in bold uppercase, but you cannot type fewer.

• Italic text indicates a generic specification, for example
  
  -OUT=/directory/filename

  Replace the generic specification /directory/filename with the actual directory and filename, for example /project/gamma.map.

  % - This symbol indicates the UNIX operating system prompt. This is simply a convention used in this guide; your site may use a different prompt. Do not type the % as part of the command line.

  <Ctrl>c - Keyboard keys appear in angled brackets < >. For example, <Ctrl>c indicates that you should press and hold the <Ctrl> key and press the letter c.

  <Return> - This key indicates a carriage return. It tells the computer to execute the command that you typed on the command line. On some keyboards this key is called Enter. (Do not confuse the <Return> key with the <Enter> key on the numeric keypad on the right side of your keyboard.)

  UNIX - This documentation set uses "UNIX" to refer to AIX, Solaris, IRIX, and OSF/1.

  UNIX Shells - The Wisconsin Package runs on both the C shell and Korn shell. When system commands differ between the two, both commands are given, marked as either "csh" or "ksh."

Screen Conventions

Screen Examples - - The screen examples included in this guide were created and captured on an X terminal using the X Windows graphics configuration.

Organizational Conventions

For Advanced Users
If you browse the table of contents, you will notice a section titled "For Advanced Users" in most chapters. The tasks in these sections are advanced user techniques and topics; they are set apart from other other tasks in the chapters so as not to overwhelm a new user. The tasks in these sections are not required for you to work effectively with the Package.

How This Guide is Organized

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This guide is divided into five chapters, followed by appendices, a glossary, and an index. Use the following table as a general guide to find the information you need in the Wisconsin Package documentation.

Table 1 (Preformatted Version)

Getting Help

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If you find that you need additional help with the Wisconsin Package, check your paper documentation or online help. GCG also has a technical support staff which you can contact by telephone, fax, or e-mail. In addition, training services are available.

Using Online Help

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Online help includes the entire Program Manual and User's Guide. Two types of help for the Wisconsin Package are available: GenHelp and GenManual. Both types include the same information, though organized differently.

• GenHelp. To access online help organized alphabetically by program name, type % genhelp.

• GenManual. To access online help in which programs are organized by function, type % genmanual.

  Within each functional category, you will find the names of the programs and their descriptions. Programs may appear under multiple functional categories. For example, you will find a description of PeptideMap in the categories Mapping and Protein Analysis.

Note: To access online help for UNIX operating system commands, type % man command_name, for example % man ls.

Using GCG Technical Support

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Technical support is available Monday through Friday from 8:30 a.m. to 5:30 p.m. Central Time. You can reach GCG's technical support staff by telephone, fax, or e-mail:

Phone: - (608) 231-5200
Fax: - (608) 231-5202
E-mail: - help@GCG.com

When you call, you should be at your computer and be prepared to provide the following information, if possible:

• Where do you use the Wisconsin Package, and what version are you running? (Type % gcgversions to display the Wisconsin Package banner, which lists the version you are using.)

• What operating system are you running the Package on? (Type % uname.)

• What hardware and, if applicable, terminal emulator are you using?

• What exactly was the command you typed and the error message returned?

• What data were you using? If possible, supply GCG with the data to replicate the problem.

• What have you done to try to solve the problem?

Make sure you supply the GCG support person with your name, e-mail address/fax number/telephone number, and the name of your company or institution.

Getting Wisconsin Package Training

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Genetics Computer Group offers training services tailored to your site.

Standard training courses include lecture and laboratory sessions. The lecture provides an overview of the Package, discussion of computer algorithms, and strategies for answering basic research questions. Laboratory sessions let you gain hands-on experience with the programs, learn how to interpret output files created, and ask questions specific to your research needs.

The training usually takes place at your site. However, small groups of users also have the option of training at GCG. The course varies between two and three days.

For more information about GCG's training services, call (608) 231-5200, fax (608) 231-5202, or e-mail Training@GCG.Com.

Using Companion Documentation

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In addition to this command-line User's Guide, the Wisconsin Package documentation set includes the following manuals. Each site receives one copy of each of these manuals.

• Program Manual. Provides complete program descriptions, including underlying scientific principles, how to use each program, and how to interpret program results. The programs are organized alphabetically. To help find the program you need, a table organizing the programs by the function is included. The functional categories are
  
  Comparison -- Pairwise and Multiple
  Database Searching and Retrieval -- Reference or Sequence Data
  Editing and Publication
  Evolution
  Fragment Assembly
  Gene Finding and Pattern Recognition
  Importing/Exporting
  Mapping
  Primer Selection
  Protein Analysis
  RNA Secondary Structure
  Translation
  Utilities -- miscellaneous

• SeqLab Guide. Provides a complete step-by-step description of how to use SeqLab. This guide also comes with a SeqLab Quick-Reference card to help you remember keyboard and mouse techniques for navigating through, selecting, and editing sequences.

• SeqLab Tutorial. Provides a step-by-step tour of SeqLab, the Wisconsin Package graphical user interface. These lessons quickly move you beyond the basics of the interface. (This manual was not ready at the release of Version 9.0.)

• Command-Line Summary. Provides a summary of each Wisconsin Package program and its parameters. (This manual was not ready at the release of Version 9.0.)

• System Support Manual. For system managers, programmers, and advanced users. Provides information on installing and maintaining the Wisconsin Package and customizing SeqLab as well as descriptions of database and system utilities.

Ordering Additional Documentation

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You can order additional copies of the documentation described above by calling (608) 231-5200, faxing (608) 231-5202, or e-mailing Doc@GCG.Com.

If you need help deciding which documentation best fits your needs, ask to speak to a technical support person before placing your order.

Photocopying or Printing Documentation

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Genetics Computer Group permits photocopying of Wisconsin Package documentation for use by institutions that hold valid License Agreements. GCG also provides the Red documentation files for the Program Manual, which you can print without permission. (For more information on the Red program, see the Program Manual.) You can buy binders and tabs from GCG to make locally produced documents more appealing.

In addition, GCG sells a service called WisPPr^(TM) (pronounced whisper)--Wisconsin Package Printing Files. The WisPPr Files service furnishes you with the most current documentation files via ftp. PostScript files are available for the User's Guide, SeqLab Guide, SeqLab Tutorial, Program Manual, and release notes. Purchasers of WisPPr must be GCG licensees and can use the files from WisPPr to produce high-quality Wisconsin Package documents on PostScript-compatible printers.

[ Program Manual | User's Guide | Data Files | Databases ]

Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com

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All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.

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