New ABI Analysis Upgrade?

C.J. Hussussian, MD cjh at helix.nih.gov
Thu Apr 7 15:44:57 EST 1994

Our lab is currently running several sequence-dependent projects and we
make heavy use of our ABI sequencer. We have found that for our work
Sequencher (GeneCodes, Ann Arbor, MI) is far and away the best assembly
program available. Much of is functionality comes from the ability to
directly download the analysis files from the ABI and compare the
chromatograms from the aligned sequences in an efficient and intuitive
way. Recently we have become aware of a possible upgrade in the ABI
analysis software that would compress the analysis files in such a way
as to render them unreadable to third party sequence assembly software
such as Sequencher. We became aware of this upgrade through our ABI
applications specialist who had contacted us about beta-testing the new
version. We explained that it was doubtful that we would be able to use
it as the files it creates would most likely be incompatible with our
assembly software and haven't heard from them since.

We have been in contact with Howard Cash, the president of GeneCodes
who verified that any change in the format of the analysis files would
create compatibility problems with Sequencher as ABI refuses to divulge
its encryption algorithm except at high price.

Does anybody know the status of this software upgrade? Does anyone know
the reason for the upgrade or any benefits of upgrading other than
compressed analysis files?

We have fully tested the current and next generation versions of the
ABI Inherit software and have found it to be insufficient for our
needs. In light of the fact that ABI does not currently offer a viable
alternative to third party assembly software, it seems to me that they
should be more lenient towards the producers of these needed programs.
Changing the format of the ABI analysis output files would reduce our
ablility to use their sequencer to rapidly obtain high quality
assembled sequences in our lab and undoubtedly others as well. I'm not
sure this would engender a great deal of customer satisfaction.

I have no affiliation with ABI or GeneCodes except as a heavy user of
their products.

C.J. Hussussian, MD                         Ph: 301-402-2029
NIH/NCHGR                                   e-mail: cjh at helix.nih.gov
Bethesda, MD 20892

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