Introduction to SeqWeb, the web inteface to GCG

February 2007 - SeqWeb is now version 3.1.2. New programs, and improved browser compatability!
Information for the beginning GCG/SeqWeb user

What's new in SeqWeb 3.1.2

What is GCG?

GCG, previously known as the Wisconsin Package, is a suite of programs distributed by Accelrys, for the analysis of DNA and Protein sequence data. ACHS maintains a GCG distribution (currently version 11.1.3) on our Dell server, watson.achs.virginia.edu

What is SeqWeb?

SeqWeb is a web-based access portal to many of GCG's programs and features. It is not a full implementation of the GCG/Wisconsin package of programs. ACHS maintains SeqWeb on our server, gcg.med.virginia.edu

Useful sites for learning to work with GCG:

From the ACHS web site, UVa users have access to the on-line GCG manual (including short notes for each program), as well as ACHS documentation

Once logged into SeqWeb (http://gcg.med.virginia.edu), users have access to online help - click on the link, "Help Topics | Support" in the upper right of the SeqWeb browser window.

Upon registering their e-mail address, UVa users may also download the GCG documentation from the Accelrys web site

Dr. Steven M. Thompson's faculty web page has access to course material and tutorials

Specific sites for SeqWeb information:

Current SeqWeb documentation is available from the web page, via the "Help" link on the upper right hand corner of the SeqWeb screen

Things to note about using SeqWeb:

With version 3.1.2 it is no longer necessary to maintain an active web connection while performing analyses. Jobs are run In Background, and the results accessed at any later session (use the "Job" Manager window).

Unlike files in your home directory account, your SeqWeb files are stored on the server itself. These files are NOT backed up, and it is the responsibility of each individual to back up his or her own files to their local machine. Also please note that you each have a finite amount of space on the server (~2Mb), so please keep track of your stored results (Managers >> Results) and remove them from the server periodically.

You may save output from SeqWeb ONLY as plain text files or HTML files. This means that you cannot import the results of a SeqWeb analysis directly into any other program, including other programs within SeqWeb. If you need to do a coordinated series of analyses, or need to add to data sets over time, then you should consider learning to use either the command line version of GCG or, it's full UNIX graphic interface, SeqLab.

For SeqWeb assistance, contact Michael Black (mblack@virginia.edu)

Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.

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