GCG software

Mike Mitchell mike at bison.lif.icnet.uk
Tue Dec 20 04:43:33 EST 1994


In article <D12pCG.5rI at murdoch.acc.Virginia.EDU>,
wrp at alpha1.bioch.Virginia.EDU (William R. Pearson) wrote:

> 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.....
>
> In my experience, the GCG package is the most comprehensive package of
> sequence analysis software available, with more than 100 programs.

We would agree that GCG is indeed comprehensive and could address most needs
for mol biologists. However, certain functions are not as well developed
as they might be. As such these can be complemented by programs such as
Nentrez and Macaw. Indeed we would advocate complementing any commercial
software tools with good non-commercial software such as MacPattern and
the aforementioned programs and say ReadSeq for sequence format
conversion. For UNIX boxes the list is long and includes such goodies as
GDE.
 
> GCG is not complete, of course.
  
But then which package is ? Our approach has been to mix and match
programs and hardware depending on available resources (which includes
ourselves).

> 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...... 

Some of us have machines as lowly as a Mac IIci and can run programs such
as Geneworks, DNAStar (also available for Windows), MacVector or
Sequencher. Other commercial packages exist for the Macintosh, and for
DOS/Windows. 

We are not convinced by the notion that most places have access to a
Silicon Graphics workstation for molecular modeling. It is more likely
that they WILL have access to at least a personal computer of some sort
(and hopefully InterNet access). In this case the first question is
whether a fast processor is available and then whether there needs to be
extra outlay for RAM, extra hard disks, CD drives.  The Macintosh programs
for example offer GUIs, databases on CDROM, and point and click multiple
sequence editing to name but a few features. The programs offer good
graphics and comprehensive analyses. In some instances the ability to
build one's own analyses is available. Network versions of these programs
are now appearing.

In any case when we consider cost there is an initial "licence" fee to be
paid and some kind of ongoing maintenance cost for ANY commercial
offering. The scale of the latter will vary depending on the deal ie
technical support, databases or programs updates.

GCG has only recently added a GUI (via X windows) otherwise you must rely
on some local guru installing or building a menu based front end for the
GCG novitiate (it's not essential but it certainly helps). Other overheads
to consider include the desire to set up and maintain weekly (or daily)
database updates

Michelle Ginsburg (Manager), Mike Mitchell (Support & Training)

Molecular Biology Software Applications Group

Imperial Cancer Research Fund, London
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