Accelrys GCG software FAQ

Table of Contents

Introduction
FAQs

Introduction

The Accelrys GCG (Accelrys Inc., San Diego, CA) is an integrated comprehensive sequence analysis package consisting of over 130 programs. This document addresses Frequently Asked Questions about the package.

FAQs

Q: What is the Accelrys GCG Package?
Q: How do I get a Bioscience UserID?
Q: Where do I buy manuals?
Q: How do I print from the Bioscience computer?
Q: How do I connect to the Bioscience server?
Q: How do I get an X-window server?
Q: How do I use Seqlab?
 Q:

What is the Accelrys GCG Package?

A:

The Accelrys GCG Package (Accelrys Inc., San Diego, CA) is an integrated comprehensive sequence analysis package consisting of over 130 programs. These programs can be categorized within the following functional groups:

  • Comparison

  • Database searching and retrieval

  • DNA/RNA secondary structure

  • Evolution

  • Fragment assembly

  • Gene finding and Exporting

  • Mapping

  • Primer selection

  • Protein analysis

  • Translation

The package allows users to conduct intensive sequence database retrieval and search, including BLAST, FASTA, HmmerSearch, that uses a profile hidden Markov Model as a query to search a sequence database and MotifSearch, that uses a set of MEME profiles to search a database to find new sequences similar to the original family. The databases that GCG supports include most major public ones of nucleic acid and protein sequences, and can be daily updated if requested. The package provides means for paired and multiple sequences alignments, evolutionary phylogeny study, fragment assembly, restriction enzyme mapping, secondary structure prediction, protein analysis, primer selection and so forth.

Using the Wisconsin Package makes it easy to work with different data formats, such as EMBL, GenBank, PIR and FastA. The Accelrys Package also makes it possible to conduct a flow of analyses from within a single interface, to save user's time by removing the need to reformat the result file(s) obtained from a previous program as an input for a next program that one wants to run.

Furthermore, GCG allows users to create new scoring matrices for sequence comparison and even to make their own databases for database search. In addition to the command line interface, most programs of GCG can be accessed through the graphic user's interface (GUI) by which user can run a program by clicking on and selecting from pull-down menus.

For more information about this software package, you may visit http://www.accelrys.com .

Available for download is a Microsoft Powerpoint presentation " [ http://help.unc.edu/?id= ] [ https://biosci.unc.edu/docs/Introduction%2520to%2520the%2520GCG%2520Wisconsin%2520Package.ppt ] Introduction to the Accelrys GCG Package " that was used in a seminar to UNC researchers by JP Jin, from the Center for Bioinformatics in April 2004.

Also available is the Microsoft Powerpoint presentation " [ http://help.unc.edu/?id= ] [ https://biosci.unc.edu/docs/GCG%26UNIX_Intro.ppt ] Introduction to GCG and Unix " that was used by JP Jin in a hands-on training in February and March 2005.

GCG is available at no cost to UNC-Chapel Hill researchers due to a site license.

 
 Q:

How do I get a Bioscience UserID?

A:

The gcg.unc.edu server is the UNC Information Technology Services (ITS) research computing platform specifically dedicated to the molecular biology application, the Accelrys GCG Package. As such, the availability of UNC user IDs on this system is strictly related to the need to access the Accelrys GCG Package software.

In order to get a userid on gcg.unc.edu, you must first get an [ http://help.unc.edu/?trail=1602,1180&type=all ] onyen account. "onyen" stands for "only name you'll ever need". To sign up for an onyen, make sure you have a PID and go to the [ https://onyen.unc.edu/cgi-bin/unc_id/services ] onyen website . Click on the button to create an onyen. Once your onyen account is functional, return to the [ https://onyen.unc.edu/cgi-bin/unc_id/services ] onyen website . Near the bottom of the page under the "Other Services" heading, follow the blue button link to subscribe to services. Login when prompted and you will be brought to the subscription page. The services available to you will be shown in the "Unsubscribed Services" box. Click the button for Biosciences services to activate your service. Make sure that bioscience services appear in the Subscribed Services box.

If there is no option to subscribe to "Biosciences services" access, you should contact .

 
 Q:

Where do I buy manuals?

A:

GCG manuals are no longer available in print form locally. GGG manuals are all online at [ http://www.unc.edu/gcg ] GCG Manuals .

 
 Q:

How do I print from the Bioscience computer?

A:

There are two ways to get printout from gcg.unc.edu (the bioscience computer). The first method is to transfer a file (regular text or print file) to your local desktop machine, such as an AFS copy or secure copy, and then print it from your local machine.

The other method is to print the file directly from gcg.unc.edu to a networked printer.

 
 Q:

How do I connect to the Bioscience server?

A:

The gcg.unc.edu Bioscience server is accessed using the SSH protocol instead of a normal telnet. To access the server, follow the steps below:

Windows Users:

  1. Download the SecureCRT client from: [ https://shareware.unc.edu/software.html#s ] https://shareware.unc.edu/software.html#s

  2. Run the SecureCRT client.

  3. Click on the Quick Connect button and fill in the fields as follows:

    • Host Name: gcg.unc.edu

    • User Name: your onyen user-id

  4. Click Connect. You will be prompted for your password, enter your onyen password and hit OK.

  5. You may now begin using the command-line interface of GCG. For help in using this interface, please see the [ http://www.unc.edu/gcg ] GCG Manuals .

Macintosh OS X Users:

  1. Download and install X11, found at: [ http://www.apple.com/macosx/features/x11/ ] http://www.apple.com/macosx/x11 .

  2. Run X11 , at the $ prompt, type in ssh -X 'your onyen'@gcg.unc.edu (where 'your onyen' is actually your onyen) and hit Enter.

  3. Type in your onyen password when prompted and hit enter.

  4. You may now begin using the command-line interface of GCG. For help in using this interface, please see the [ http://www.unc.edu/gcg ] GCG Manuals .

All other Macintosh Users:

  1. Download and install MacSSH from [ http://www.macssh.com/ ] http://www.macssh.com .

  2. Run MacSSH, and from the File menu, select Open Connection.

  3. Type in gcg.unc.edu when you are prompted for the host name.

  4. A window will pop up and prompt you for your username and password. Enter your onyen and your onyen password, and hit OK.

  5. You may now begin using the command-line interface of GCG. For help in using this interface, please see the [ http://www.unc.edu/gcg/ ] GCG Manuals .

 
 Q:

How do I get an X-window server?

A:

If you want to use the GCG GUI (Graphical User Interface), which GCG calls Seqlab, you must do several things.

First, you must have X-window server software for your local computer. Currently, we recommend X-Win32 for Windows and X11 for Macintosh OS X. There is no free X-windows server for Mac OS 9 or earlier currently available. ITS has a site license for X-Win32. To get X-Win32 go to [ https://shareware.unc.edu ] http://shareware.unc.edu . To obtain X11, go to [ http://www.apple.com/macosx/features/x11/ ] http://www.apple.com/macosx/x11 .

After you have installed the X-window Server software, you can then follow the following steps to start the GCG GUI.

  1. Start X-Win32 or X11.

    • For a Macintosh, do the following:

    • At the $ prompt of the X11 terminal window, type +xhost gcg.unc.edu .

    • For Windows, do the following (these steps only need to be taken once when you install X-Win32):

    • After starting X-Win32, you should see a small blue X icon in your system tray, right-click on it and select X-Config.

    • Under the sessions tab, click the Add... button.

    • Select "XDMCP" as your connection method and click Next.

    • In the window that appears next, type gcg.unc.edu into the host name field, gcg.unc.edu into the session name field, and select "Query" as the XDMCP mode.

    • Keep the Default options for all other settings and click Save.

    • Now that you are back at the initial window, select the Security tab.

    • Click the Add... button and type gcg.unc.edu into the window that has just appeared. Hit OK.

    • In the main X-Win32 config window, hit OK to save these settings.

  2. Start your SSH client, connect to gcg.unc.edu, and login.

  3. type: xterm & (Macintosh users may skip this step)

  4. type: seqlab &

  5. After a few seconds the SeqLab windows will appear.

 
 Q:

How do I use Seqlab?

A:

Please view our [ https://biosci.unc.edu/software/gcg/SeqLab.htm ] Seqlab Tutorial to become familiar with the Seqlab interface. For more in depth information, you can refer to the [ http://www.unc.edu/gcg/gcgmanual11.0/seqlab.html ] Seqlab Manuals .

 

[ http://its.unc.edu/research-computing.html ] Research Computing home page

Copyright 2002-2007 The University of North Carolina at Chapel Hill.

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