Fw: Other: EMBOSS versus GCG?

Rory Bowden r.bowden at vir.gla.ac.uk
Thu Nov 14 15:36:23 UTC 2002

This on the 'evoldir' list, which is the main international mailing list in
evolutionary biology. Would anyone like to make any comments for me to pass

while I'm definitely not in Canada I would say that this question is likely
to come up here (in the UK) at the institutional if not research council
level. Does anyone have an opinion they'd like to articulate e.g. about
whether EMBOSS is ready to supplant GCG for end-users.

Rory Bowden
MRC Virology Unit
Glasgow UK

----- Original Message -----
From: "EvolDir" <evoldir at evol.biology.mcmaster.ca>
To: <r.bowden at vir.gla.ac.uk>
Sent: Thursday, November 14, 2002 9:34 AM
Subject: Other: EMBOSS versus GCG?

> Since its inception as the "Wisconsin package" in the early 1980s, the GCG
> suite of programs have provided a continuously improving "gold standard"
> for evolutionary bioinformatics software. The GCG suite is featured
> extensively in the latest bioinformatics textbooks (e.g. Mount) and in
> software reviews (e.g. The Scientist, August 19). Although some individual
> GCG programs have been surpassed by others, their range and flexibility,
> permitting linkage of programs together in innovative ways, has no current
> equivalent.
>       Recently, "open source" advocates have pointed to the EMBOSS suite
> providing a free alternative to the commercial package (supplied by
> Accelrys, with whom I have no financial connection). It is my impression
> that GCG is in a different league. For example, compare the GCG program
> "Window" with its proposed EMBOSS alternative "Freak":
> TASK: Determination of the number of occurences of a motif in a sequence
> window.
> GGC program WINDOW
> 1. Allows up to 6 motifs at a time
> 2. Outputs absolute values and has a variety of other output options.
> 3. Extensive input menu
> EMBOSS program FREAK
> 1. Allows only 1 motif at a time.
> 2. Outputs a calculated fraction.
> 3. Very limited input menu.
>        However, in Canada the open-source agenda has won out. In April
> the publicly-funded, Halifax-based, Canadian Bioinformatics Resource (CBR)
> abandonned GCG, apparently with the consent of the Canadian evolutionary
> bioinformatics community. In this respect, I would be interested to hear
> from concerned parties in Canada with respect to the following questions:
> 1. Does your institution (or do you yourself) support GCG, so that you do
> not need CBR to supply GCG?
> 2. If you do not have independent access, do you find EMBOSS a suitable
> substitute for GCG?
>        That Canada, which has spent hundreds of millions on genome
> projects, cannot give its researchers and their students a choice from
> among the relatively-inexpensive software packages that are available to
> analyze genomics data, seems to me very strange.
> Donald Forsdyke, Department of Biochemistry,
> Queen's University, Canada
> http://post.queensu.ca/~forsdyke/bioinfor.htm

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