[Nov 23, 2009 14:09] Web access to Microsoft Live@edu accounts now works.
GCG/SeqWeb is no longer available at UVa (as of July 1, 2009)
In June 2008, Accelrys discontinued support, development and further distribution of the GCG suite of programs. Due to licensing issues, GCG will not be released to the public domain as open source software.
GCG at UVa has been discontinued as of July 1st, 2009.
Researchers who still need a general sequence manipulation set of program can use the following web resources:
- NCBI web resources
- EMBL/EBI web resources
- ExPASy web resources
- Institut Pasteur web resources
- The San Diego Supercomputer Center's biology workbench, a free online suite of tools and databases for DNA and protein sequence analyses.
Program suites that can be run on individual personal computers
EMBOSS
EMBOSS is a collection of programs analogous to that found in GCG. It can be compiled under UNIX, Linux and Apple OS X (developers tools must be installed) and used as a collection of command line tools. Also, several graphic interfaces exist for EMBOSS, and the semi-official one is known as JemBoss (semi-official in that it is included with your download of EMBOSS, but JemBoss has a distinct development team). An uncompressed download of EMBOSS includes a script file, "install-jemboss-server.sh" which can be used to install a standalone copy of EMBOSS, the associated (optional) EMBASSY packages, and JemBoss. Mac OS X users will need to know the path to their java installation (currently for OS X 10.5.5 = /System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home). There is also a Windows version of EMBOSS available, or the command line version may be compiled and run on Windows under cygwin (a Linux-like environment for Windows).
EMBASSY is a collection of programs that may be installed with the EMBOSS package (for licensing reasons, the EMBASSY packages cannot be bundled directly with the EMBOSS programs).
Anonymous guest access to a web version of EMBOSS is available at EMBnet.
Programs that can be used as standalone as well as with EMBOSS programs:
- Clustalw2 and ClustalX - clustalw is a command line multiply alignment application (which can be used in place of GCG's PILEUP program), and clustalX is a GUI interface to clustalw available for Windows and Apple OS X. Clustalw can be run online at EBI or on your local computer by clicking EBI's “Download Software” link to access their anonymous FTP server.
- Primer 3 is a command line program for designing PCR primers and hybridization probes and is called by the EMBOSS program primersearch.
- PHYLIP, the Phylogeny Inference Package, is available from the developer's web site at the Univ. of Washington as source code and as precompiled programs for Windows and Apple OS X. It can also be built as part of EMBOSS by downloading the EMBASSY packages. PHYLIP will also continue to be available on ACHS machines (watson.achs.virginia.edu).
You can read our summary guide to compiling EMBOSS. Windows users should follow the EMBOSS download link under the "Platform-dependent notes " section to download a JemBoss installer file for windows.
The Sequence Manipulation Suite (SMS2)
SMS2 is a collection of java scripts which will provide web-linked interfaces to programs available on the internet, many of which can be used in place of GCG programs. SMS2 unpacks on your local computer as a folder of html files. Open the file "index.html" in your local browser to mirror the site as shown in the preceding link, and use the tool links on the left side bar to run analyses.