Automatic Sequencing by Capillary Electrophoresis

John Barlow john_q_barlow at hotmail.com
Wed Aug 18 15:46:49 EST 1999

Here is some specific information on the result of a recent test on the Beckman 
CEQ 2000.  Another user (from Europe) reported exactly the same problem to me.  
I hope that Beckman Project Managers read this group and that they will try to 
get their programmers to work harder.  Present software is simply inadequate 
and possibly was never shown to power users before releasing to the public.

We definitely need a good instrument to compete with ABI products.  So far, 
after the demise of the ALF and the fallout of Amersham with Visible Genetics 
over the crappy quality of their sequencers, the CEQ 2000 may be the last hope. 
 You all know by now that the LiCor instruments have very vocal, albeit rare 
supporters and the final word on LiCor is difficult to come by.

By the way, the higher signal that we get with the ABI 377 than with the CEQ 
2000 can be attributed to the BigDye technology.  It is probably the best thing 
since sliced bread.


We did some more testing on the CEQ.  Specifically, we sequenced about forty
435 bases long PCR products.  Next we did the same thing that we do with the
results from ABI 377 XL - we transferred the trace files to a PC running the
latest version of SeqMan II from the LaserGene (DNAStar) suite.

In SeqMan, we loaded the traces (in SCF format for the CEQ and in the ABI
format from the 377), trimmed ends using the Medium option, and assembled
the contig.  Next, we scanned the contig for ambiguous positions.

The results from the Beckman were, unfortunately, quite disastrous.  First, we
get a much higher (10 fold difference) signal with the ABI 377.  Next, the
basecalling on the Beckman is very bad, just like we have observed it last
March and May.  The problem is that when a position is ambiguous, the ABI
basecalling will assign an "N".  Rarely, the ABI basecaller would fail and
not call a base at all.  In our hands, this happens only on one strand and can 
be corrected by comparison with the complementary strand in SeqMan.  On
the other hand, the CEQ basecaller will frequently assign a wrong base where
the ABI will show an "N".  In addition, the CEQ basecaller missed about 5%
of the positions.  Proof reading with the CEQ data alone would not be
possible, because of the low signal.  We had about 4 people testing these
traces and all decided against the CEQ in favor of the 377.

In article <7pa4qf$ggf at net.bio.net>, srlasky at cellworks.mbt.washington.edu 
>"Stephen R. Lasky" wrote:
>> I would like to refer you to the post made by John barlow 07/21/1999
>> where he gives a good review he recieve in response to which sequencer
>> to buy.
>> srl
>Boy, that didn't make any sense..  Try:  See the post by John Barlow
>7/21/99.  He reviews the responses he received on the Beckman.
>Stephen R. Lasky, Ph.D.                 #
>University of Washington                #
>Department of Molecular Biotechnology   #
>srlasky at u.washington.edu                #

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