Before You Begin

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

Table of Contents

Introduction

Interfaces to GCG

Using this guide

Conventions used in this guide

How this guide is organized

Getting help

Using online help

Using a different web browser to access online help

Getting technical support

Using companion documentation


Introduction

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GCG is an integrated package of over 150 programs that allows you to manipulate and analyze nucleic acid and protein sequences. Scientists from all over the world have collaborated to develop and refine GCG, making it a flexible tool with which to analyze your sequence data.

 

 Among its many features, GCG gives you access to

·       Comparison. Compare two or more sequences. Create, edit, display, and analyze multiple sequence alignments.

·       Database Searching and Retrieval. Search nucleic acid or protein sequence databases for sequences similar to your query sequence or sequence pattern.

·       DNA/RNA Secondary Structure. Predict and display optimal and suboptimal DNA or RNA secondary structures.

·       Editing and Publication. Enter sequences from a digitizer or a keyboard and edit them.

·       Evolution. Determine and display evolutionary phylogenies from multiple sequence alignments.

·       Fragment Assembly. Manage and assemble nucleotide sequence fragments in a sequencing project.

·       Gene Finding and Pattern Recognition. Recognize terminators, repeats, protein coding regions, and other consensus patterns.

·       HMMER (Hidden Markov Model). Create a profile hidden Markov model (HMM) that represents the similarities in related sequences and use the model for database searching, sequence alignment, or generating random sequences.

·       Mapping. Calculate and display restriction digests and simulate RNA fingerprints.

·       Primer Prediction. Predict optimal primers for PCR reactions.

·       Protein Analysis. Identify sequence motifs in protein sequences and make predictions about peptide isolation.

·       Translation. Translate nucleic acids into proteins and backtranslate proteins into nucleic acids.

Interfaces to GCG

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GCG provides these interfaces for your analysis needs:

·         SeqWeb. Provides a web interface to a core set of GCG programs.

·         SeqLab. Based on X Windows, SeqLab provides a point-and-click multiple sequence editor and annotation tool with access to all GCG programs.

·         Command-Line. Each program steps you through the required parameters it needs to run. Add optional parameters to the command-line for customized analyses. Scriptable command lines provide the ability to do repetitive and numerous analyses.

·         SeqMerge. SeqMerge is GCG’s powerful new fragment assembly application with an X Windows graphical user interface. SeqMerge allows you to intuitively assemble fragments from a sequencing project into contigs, or into alignments of overlapping fragments.  From the contig, SeqMerge also creates a consensus sequence representing the underlying sequence from which your fragments were derived. 


Using this guide

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This User's Guide provides information about GCG commands and concepts. It is designed to be both a beginner's guide to working with GCG 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 GCG 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 GCG 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 efficiently extract the information in which you're interested.

Tip: This symbol indicates a helpful hint which might make your work easier.

Text Conventions

A special typeface (Courier New, 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 in non-plus programs, 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.

·         To invoke command-line parameters in plus programs, bold Courier New text indicates the number of letters you can type (for example -begin=93,  -beg=93). You can type either -beg=93 or -begin=93 to invoke the parameter.

·         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, Tru64 (OSF/1), and Linux.

 

UNIX Shells –

 

GCG 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 sections. The tasks in these sections are advanced user techniques and topics; they are set apart from other tasks in the sections so as not to overwhelm a new user. The tasks in these sections are not required for you to work effectively with GCG.

How this guide is organized

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

If you're interested in

Turn to

An overview of the operating system

Section 1, Getting Started

Starting the GCG

Section 1, Getting Started

Specifics about using sequences

Section 2, Using Sequences

Databases

Section 2, Using Sequences

Learning about the basic concepts you will need to use the GCG programs

Section 3, Using Programs

Learning how to run specific programs

Program Manual and Command-Line Summary

Finding out about different data files, for example scoring matrices and restriction enzymes

Section 4, Using Data Files
or Appendix VII of the Program Manual

Learning more about GCG programs that produce graphic output, how you can use and manipulate that output, and what graphics configuration languages are available

Section 5, Using Graphics and Appendix C, Graphics

Printing ASCII or graphic files

Section 3, Using Programs and Section 5, Using Graphics

A list of GCG programs organized by function

Appendix A, Short Descriptions, Functional table of contents list of the Program Manual, and Programs by Function section of the Command-Line Summary

Basic guidelines for using the text editor vi

Appendix B, Text Editor Basics

Definitions of some terms found in this guide

Glossary


Getting help

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Accelrys Scientific Support is available for assistance if you should encounter difficulty in using our products, or if you need assistance in their use. If you cannot find the information you need in this guide or the online Help, visit the Accelrys Advantage web pages or contact Accelrys Support.

Using online help

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The online help for GCG is in HTML format and provides access to the Program Manual, User's Guide, User Release Notes, and data files.

 

You can choose between two types of help: 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. Programs may appear within multiple functional categories.

 

The commands % genhelp and % genmanual automatically launch Lynx, a text-only web browser, which enables you to view the online help. (To use a web browser you are more familiar with, see "Using a Different Web Browser to Access Online Help" later in this section.)

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

Navigating in Lynx

To navigate in Lynx, use the following keys:


To do this

Press

Highlight next link

<Down Arrow>

Highlight previous link

<Up Arrow>

Follow the link

<Return> or <Right Arrow>

Go back to previous document

<Left Arrow>

Go to top of document

<Ctrl>A

Go to end of document

<Ctrl>E

Page down

<Space Bar>

See a history list of previous links in your current session

<Delete> or <Backspace>

Note: If your arrow keys do not work, press “o V <Space Bar> <Return> r”.
 
(That is, press lowercase letter "o", capital letter "V", <Space Bar>, <Return>, lowercase letter "r".)

This key combination will put Lynx into vi mode. You can then use the following keys for navigating:

h - Go back to previous document
j -  Highlight next link
k - Highlight previous link
l -  Follow the link
H - Get help

You may also find the following keys useful:

To do this

Press

Get help

H, h, or ?

Return to main GCG help page

m

Print

p

Quit Lynx

q

Search the current document

/

Reload document and refresh screen

<Ctrl>R

Cancel a transfer in progress

z

For a list of other helpful keystroke commands, see the topics "Lynx Users Guide" and "Key-stroke Commands" in Lynx's online help.

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

Using a different web browser to access online help

You can use a web browser you are more familiar with, such as Netscape or Internet Explorer, to access online help.

The first step is to get the URL (Universal Resource Locator) for the online help at your site. To do so, type % gcgversions.

 

 

Your system manager should have inserted the URL for your site's online help in the GCG banner. (In this example, the URL appears toward the bottom of the screen).

After getting the URL for online help, choose between the following:

·       If you have a Macintosh or a PC or a UNIX workstation:

1.    Set a bookmark to the online help location at your site.

2.    Start the browser of your choice and set the location of the online help files. For example, from Netscape select Open Page... from the File menu and type the URL for online help.

·       If you have a UNIX workstation or an X terminal:

1.    Define an alias for the online help command. We recommend that you do not overwrite the current commands of % genhelp and % genmanual. Rather, define new aliases, such as nethelp or gcghelp. Consider the following example:

% alias nethelp netscape http://www.accelrys.com/support/bio/genhelp/

To save this definition and make it available each time you log in, adds the command above to one of the following files: .gcgrc (csh) or .gcgrc.ksh (ksh). For more information about command procedures, see "Working with Command Procedures" in Section 3, Using Programs.

Getting technical support

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You can reach technical support staff by telephone, fax, or e-mail:

US

Toll Free: +1 800 756 4674
Tel: +1 858 799 5509
Fax: +1 858 799 5102

E-mail: support-us@accelrys.com

 

Europe

Tel: +44 1223 228822
UK local rate: +44 845 741 3375
Fax: +44 1223 228501

E-mail: support-eu@accelrys.com

Japan

Tel: 81 3 3578 3861
Fax: 81 3 3578 3873

E-mail: support-japan@accelrys.com

 

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

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

·         From what operating system are you running GCG? (Type % uname.)

·         What interface are you using (command-line, SeqLab, or SeqWeb)? 

·         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 the support staff with the data to replicate the problem.

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

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


Using companion documentation

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In addition to this command-line User's Guide, GCG documentation set includes the following manuals in PDF format on CD, which is provided along with the product.

 

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 function is included. The functional categories are

Comparison -- Pairwise and Multiple
Database Searching and Ret
rieval -- Reference or Sequence Data
Editing and Publication
Evolution
Fragment Assembly
Gene Finding and Pattern Recognition
HMMER (Hidden Markov Model)
Importing/Exporting
Mapping
Primer Selection
Protein
Analysis
DNA/RNA Secondary Structure
Translation
Utilities -- Miscellaneous

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

SeqLab Guide. Provides a detailed description of how to use SeqLab. This guide also includes two copies of 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 chapters quickly move you beyond the basics of SeqLab's interface.

SeqMerge. SeqMerge is GCG’s powerful new fragment assembly application with an X Windows graphical user interface.  SeqMerge allows you to intuitively assemble fragments from a sequencing project into contigs, or into alignments of overlapping fragments.  From the contig, SeqMerge creates a consensus sequence representing the underlying sequence from which your fragments were derived. 


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


Technical Support: support-us@accelrys.com, support-japan@accelrys.com,
or support-eu@accelrys.com

Copyright (c) 1982-2005 Accelrys Inc. All rights reserved.

 

Licenses and Trademarks: Discovery Studio ®, SeqLab ®, SeqWeb ®, SeqMerge ®, GCG ® and, the GCG logo are registered trademarks of Accelrys Inc.

 

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.

www.accelrys.com/bio