Hi folk -
I'm a bit late on this thread because I've been up at Rutgers attending a
DIMACS genomics workshop (it was great!), but I would like to add my voice
to the others in following up David Mathog's GCG questions last week.
In my opinion an integrated suite of programs such as the Wisconsin
Package is still the best way to do sequence analysis and SeqLab,
especially it's Editor mode interface, ala Steve Smith's GDE, is by far
the best way to deal with multiple sequence datasets that I've ever used.
It is NOT simple and does require a pretty intensive introductory tutorial
to get people accustomed to it, but powerful things seldom are simple, and
it is WAY more comforting to users than the command line. In comparing it
to other sofwares, I've not yet found a WWW interface capable of handling
large multiple sequence datasets reliably and, has been repeatedly pointed
out, desktop products are WAY too expensive per user in a large
institution compared to a client/server solution like SeqLab, nor have I
found one anywhere near as powerful. I certainly hope that GCG continues
as a viable company producing SeqLab and, hopefully, the Pharmocopeia
acquisition will help assure that.
As for SeqWeb the situation is totally the opposite. I can say few
positive things about it - sure it's an easy way to run the Wisconsin
Package - but for what it can do, why not just use the resources for free
on the WWW. We do NOT buy it and I, personally, don't think it's worth
the money. My apologies to all GCG personel reading, just my two cents.
Regarding support issues and code availability - GCG continues to provide
superb customer support. Lynn Miller and her group are courteous, prompt,
and knowledgeable - the best in the business that I've ever interacted
with! Not having free code is a drag, but, as has been pointed out, no
other commercial product gives their code away either. And I think that
you can still purchase it from them as their SDK product, though that may
have changed (please correct me if it's no longer available). As for
sequence and database size restrictions, they've done a pretty good job of
keeping up with it. Restrictions now include: 2 GB .seq and .ref database
sections and 350 Kb single sequences (longer entries cut into overlaps).
I can't comment on SeqMerge other than to say it looks really slick in
demonstrations. We haven't purchased it, though we are toying with the
idea. I'm pretty sure that the industry standard is still
phred/phrap/consed but it sure would be nice to have a system integrated
to SeqLab and easier to use than their old Fragment Assembly System, which
does work within SeqLab but does NOT use the SeqLab Editor for
assembly/editing and, as most of you realize, is not the most powerful nor
friendliest assembly program to teach people. At least SeqLab DOES import
ABI trace binary files and allow you to see the trace info with a viewer.
So, is SeqMerge worth the price - don't know, but maybe . . . .
Cheers - Steve
Steven M. Thompson
A C T G stevet at bio.fsu.edu
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