GCG software

William R. Pearson wrp at alpha1.bioch.Virginia.EDU
Mon Dec 19 14:41:04 EST 1994

In article <1994Dec19.170032.23277 at midway.uchicago.edu> rmoldwin at midway.uchicago.edu writes:

>   Can someone tell me what are the advantages of the GCG MB package over
>   the high-end MAC or Windows packages, or programs like MACAW and
>   Network Entrez?.  Why do some labs seem to prefer this software,
>   even though it runs on very expensive hardware?

In my experience, the GCG package is the most comprehensive package of
sequence analysis software available, with more than 100 programs.
Several programs are available to address virtually any question one can
imagine, from the size of bands in a tryptic digest of a protein to RNA
hairpin folding to sequence assembly to similarity searching, multiple
alignment, and evolutionary trees.  While it is certainly true that many
of these functions can be cobbled together from various publically
available sources for a Mac or Windows machine, the GCG package is more
comprehensive, better integrated, far better supported, and far far
better documented.

GCG is not complete, of course.  The multiple alignment strategies used
in MACAW are not availble in the GCG package (or any other commercial
package that I am aware of).

GCG does not require very expensive hardware.  It will run just fine on
a $6,000 Sun workstation (with another $1,200 for 2 GB of hard disk) and
will run very fast on a $12,000 Dec Alpha.  Alternatively, most places
have access to a Silicon Graphics workstation for molecular modeling,
and the cost can be very modest for adding a few GB of disk in return
for use of the machine for GCG.  For any location with more than two
labs doing sequence analysis, it is certainly cheaper to share the cost
of a Unix workstation and the GCG software vs. buying three or more
Mac's/PC's and multiple licenses for commercial microcomputer software.

Bill Pearson

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