ABI 373 DNA Sequencer reponses

Paul Morrison morrison at FARBER.HARVARD.EDU
Fri Oct 1 12:13:29 EST 1993

bio-netters, I queried the net a few weeks ago and here is a brief
compilation of the responses.
The query:
I have an ABI 373 DNA sequencer and use 3rd party software (Sequencher 2.0)
to build contigs and analyze the sequences and chromatograms that the 373
produces. Has anyone who is in the process of purchasing a 373 been told
that in the future the chromatograms will be compressed or encrypted which
_might_ make it unusable with other software? I will post a follow-up
comment if this turns out to be true.
The responses:
A scattering of responses that basically said that they had been told by
ABI that it would be unwise to purchase 3rd party software for down-stream
analysis of data from the 373 because ABI wouldn't guarantee that someone
else's software would work when the 373 software is updated. Some responses
said that the ABI rep mentioned encrypting the files to fool these other
companies. This kind of response came from north and south of the Mason
Dixon line and from both sides of the Atlantic so it did not come from one
overzealous ABI rep. Bruce Roe's response summed it up the best:
        I've heard this rumor for years now, especially after we and
others figured out the format for the data produced by the 373A.  At
one point they released software to produce the data with a different
delimiter in it ( '>' vs '<' ) and it took us about 10 minutes to figure
out what they did.
        Folks that produce software to read the ABI data (Staden, Sequencher,
and DNA-Star for example) are pretty smart and will figure out how to
read the ABI data even if ABI were stupid enough to do something like
that. So not to worry.
        It is of GREAT benefit to ABI to have others working on improving
data analysis software as they will be able to sell more machines and more
ABI's response: No they would never encrypt the data. Future upgrades which
will compress the chromatograms might make other software unusable so they
sell a communications toolbox so that nobody is caught off guard. If a
company decides not to buy the toolbox because it is too expensive then
they might have some compatibility problems.

My response: So is there a problem? Doesn't seem to be a big one. I agree
with Bruce Roe completely that these programs are a benefit to not only the
researchers but to ABI. Right now I think that ABI's downstream analysis of
the sequence data out of 373 is inferior to these other programs and since
that is the case they should spend more time focused on the program that
creates the data. Right now if my sample is a short PCR fragment, is CA or
GC rich, or if my gel runs a tad too fast or too slow, I end up throwing
away data that would be fine if the Analysis program was less rigid. So as
Bruce said, ARE YOU LISTENING ABI??? Stop putting the scare into companies
that are really doing you a favor and put some more time and effort into
the program that counts. You would end up selling more machines, more
reagents. And we would all be better off if there was a user base of 10,000

Paul Morrison   Dana1030
Molecular Biology Core Facility 
Dana Farber Cancer Institute
44 Binney Street
Boston, MA 02115
p_morrison at dfci.harvard.edu
morrison at farber.dfci.harvard.edu

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