GCG current version feedback

Simon Andrews simon.andrews at bbsrc.ac.uk
Wed Feb 28 05:06:40 EST 2001

David Mathog wrote:

> We've been running 8.1 for years and are considering "upgrading" to the
> current version, primarily to obtain access to SeqWeb and SeqLab.  

I've certainly found the Seqlab has been a very useful tool (especially
the rsf file format).  We're encouraging all our users to try it - most
students aren't happy just using a command line interface these days.

> It isn't
> entirely clear that we'll do this, because near as I can remarkably little
> else has been added to the package since 8.1 that isn't also available for
> free, with source code, from the original authors (BLAST 2.x, for
> instance.)

The addition I use most (apart from rsf support) was the addition of
Meme and Motifsearch (HMM type fragment searches from unaligned
sequences).  I think these are also available separately, but it's still
nice to have all the programs integrated into one large package.  It's
the ability to integrate between different programs which still makes
GCG so useful.

> Plus going to the current version means giving up our custom
> GCG based code, our custom driver level modifications, and the expanded 500
> Kb sequence size limit.
> So a bit of feedback is requested.
> 1.  What's it like dealing with GCG these days?
> 2.  How is the turnaround time on maintenance requests (crucial if we go
>        this way since wouldn't be able to maintain it ourselves anymore.)

I believe you are still supplied with source code but are not allowed to
use it elsewhere.  You may still be able to do minor bug fixes (I may
well get squished by GCG on this one!).  We've not experienced many
problems - probably due to the fact that most programs in the package
have been around for long enough that bugs have been ironed out!  GCG do
still put out point releases to fix bugs though many months can pass
between releases.

> 3.  Do "naive" users get along ok with SeqWeb or SeqLab, or are they just
>       as lost with those interfaces as most now are with the command line?

Haven't tried SeqWeb.  Seqlab is fine once you've got the idea of how it
thinks, but it's not intuitive for new users.  We find that a days
introductory course to Seqlab will get most people up and running.  It's
nice because it presents all of the programs and options to you so you
don't have to remember as many program names / command line switches. 
The editor and graphical capabilities with rsfs are good too.  On the
down side, it's file handling isn't brilliant.  If people don't tidy up
after themselves (which many don't) they can get their file space into a
right mess.  It also has an unfriendly way of performing analyses on
parts of sequences (you can't specify part of a sequence to use after
you have opened the window for the analysis program). It can also be
frustratingly slow for some simple analyses (probably due to the
overhead of opening the relevant X-windows).

> 4.  Is SeqMerge any better than phred/phrap/consed?  Is it so much better
>       that it's worth the price?

We don't use it - we try to encourage people to use Staden, which is
excellent for this kind of work.

> 5.  What alternatives to GCG, if any, have you adopted?

We are now running EMBOSS alongside GCG
(http://www.uk.embnet.org/Software/EMBOSS/).  It's freeware, source code
is supplied, there are no intrinsic limits on sequence sizes, it accepts
(and writes) a wide variety of file formats.  It's getting towards the
stage where it could be a replacement for command line gcg.  It's was
originally written by the crowd who did the EGCG, who started EMBOSS
when GCG went closed source.  There is a web interface, but no finished
X-interfaces as yet (though a couple are being written).


> and just slightly off topic
> 6.  Would you be happier with the product if you had access to the source
>       code?

Personally, not any more.  EMBOSS gives an open source alternative for C
code to study, and most of the small analysis programs I hack together
tend to be in Perl.  Given the state of the competition I wouldn't be
surprised if GCG were to slowly fade away over the next few years.  The
owners are likely to switch their attention to desktop packages such as
Omega, where the next lot of money will be made.

Just my (personal!!) opinions


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