New ABI Analysis Upgrade?

Dr. P.L. Taylor ptaylor at crc.ac.uk
Fri Apr 8 06:01:15 EST 1994

C.J. Hussussian, MD (cjh at helix.nih.gov) wrote :

>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.

Yes, I've been discussing this today with my local ABI representative.  ABI
do produce a software development kit which allows software to read the new
file format.  It's free to non-commercial developers, but if your software
is distributed for money you have to pay.

As the author of GeneJockeyII, which reads and extracts information from
ABI sample files, I'm going to have to modify my program to deal with this.
My distributor, Biosoft, is currently negotiating with ABI to obtain a copy
of the development kit, however, knowing ABI, I rather expect that the fee
will be excessive.  If this should happen it will be necessary to crack the
new file format and write my own routines to decompress the data.  (It's a lot
of work, but after all, all the existing non-ABI programs which read this data
were made by people who cracked the original file format, since ABI has always
considered this information as proprietary, and refused to release it.)

Perhaps the authors of Sequencher, DNAStar, MacVector and myself should get
together to discuss a joint approach here.

It would make far more sense, however, for ABI to encourage third-party
software development by publishing the file format.  ABI would lose nothing
by this, and would avoid causing considerable anguish to their users.

Phil Taylor
mbplt at seqnet.dl.ac.uk
ptaylor at hgmp.mrc.ac.uk

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