Automated Sequencer

Peter Gegenheimer peterg at rnaworld.bio.ukans.edu
Mon Dec 19 18:07:33 EST 1994


In <lwashing-1512941538010001 at raven.bio.indiana.edu>, lwashing at sunflower.bio.indiana.edu (Lawrence Washington) writes:
>In article <3cn8p5$nfv at mserv1.dl.ac.uk>, Erdmann Dirk MSM PH225
><dirk.erdmann at chbs-msm1.chbs.MHS.CIBA.COM> wrote:
>
>> Dear Netters,
>> 
>> our department is going to buy an automated sequencing system. We want to 
>> buy either the ABI 373A, the "ALF" from Pharmacia or the Li-Cor 4000. The 
>> last one is relatively new on the european market and I know nobody having 
>> one.
>> Here my question: does anybody know the advantages/disadvantages of the 
>> three systems under discussion? I would really appreciate to get a 
>> comprehensive comparison of the three systems.
>> Thanks a lot.
>> 
>> Dirk
>> 
>> Dirk.Erdmann at chbs.mhs.ciba.com
>
>Dear Dirk,
>
>   The companies you mentioned will readily send you literature about
>their systems on request and (at least here in the States) they are also
>happy to send representatives to give presentations and sales pitches. 
>With the information the companies give you should be able to put together
>a list of pros and cons vis-a-vis your needs.  A year ago we spent a LOT
>of time talking with those three companies and it was my experience that
>we generally got an honest assessment of the system9s capabilities.  The
>reps are also well informed about their competition so it is helpful to
>quiz them about each other (they love this).  Also check the bionet
>archive for the many discussions on this subject.
>   Advantages/disadvantages?  Here are some very simplified
>characteristics that I recall from our search. 
>   ABI9s sequencer has been around the longest and has many users so many
>of the bugs have been worked out. But it is expensive to purchase and
>operate and in our experience the quality of their service support is
>unpredictable.
>   Pharmacia claims to be very simple to use (I have never tried it).  But
>some of the gel apparatus parts are very expensive, and I personally
>dislike the chromatogram style of data presentation.
>   Li-Cor is relatively inexpensive to operate, gets very long reads (over
>800 bases routinely) and the infrared dye approach has intrinsic
>advantages.  And the data image looks like a traditional sequencing gel. 
>But users are restricted to labeled primer protocols. (Li-Cor is working
>on an internal labeled dATP technique, have been for at least a year now,
>and it still does not work).
>   This is not enough information for you to base your decision on, but
>maybe it will help get you started.  I think that all three systems that
>you mentioned are probably very good.  You just have to decide what fits
>your department best.
>   By the way, we bought the Li-Cor system and have been happy with the
>decision.  If you have any specific questions about it that you would
>rather ask a user than the company you may contact me.  Good luck.
>
>Lawrence Washington
>Indiana Institute for Molecular and Cellular Biology
>
>-- 
>Lawrence Washington
>Indiana University
>Institute for Molecular
> and Cellular Biology

We, too, have just purchased a LI-COR 4000. I decided on the basis of examining 
the  literature from all 3 mfrs that LI-COR was clearly superior technically. 
Our working experience is consistent with this appraisal. I will post a detailed
description of the LI-COR instrument later, but I'd like to make a few comments.
1) On its first run right out of the box, our machine read over 900 bases
(700 fully-automatically; 915 with manual assist beyond that) from plasmid DNA
prepared by a faculty member here. (At LI-COR, they routinely read 1000-1200
bases.)

2) Technical support is fast and responsive.

3) The IR laser lets you use plain glass gel plates rather than ones which
cost $300 each. The detector is a miniature confocal 'scope, so 
the machine can focus precisely in the center of gels of any thickness. The 
laser also lasts 10 times longer than those used by ABI or Pharmacia.

4) The multitasking software controls the gel unit, interprets the sequence in 
real time as its being acquired, AND lets you look at previously-acquired data, 
all simultaneously. The license includes several copies of the base-calling 
software, so users could work on their data at remote terminals (Ethernet & 
Novell or TCP/IP connectivity can be factory-installed).

5) The raw data is an autorad-like image of the gel which can be saved as a TIFF
image for analysis (i.e., if its a RFLP gel, mobility-shift gel, etc.), OR can 
be converted into the standard chromatogram-like format.

6) I have heard only good things about LI-COR and ABI; I have heard unfavorable 
comments about Pharmacia.

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