GCG Wisconsin Package The GCG Wisconsin Package (Accelrys Inc., San Diego, CA) is an integrated comprehensive sequence analysis package consisting of over 130 programs. The package allows users to conduct intensive sequence database retrieve 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 as well 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 Wisconsin Package also makes it possible to conduct a flow of analyses from within a single interface, so as 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, the 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 "Introduction to the GCG Wisconsin 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 "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, so if you are interested in using this application, email
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