Automated DNA Sequencing - Best buy?

Fred Locklear fred.locklear at med.umich.edu
Fri Oct 22 13:53:06 EST 1993


Subject: Automated DNA Sequencing - Best buy?
From: Dr. M.F. Grahn, mgrahn at uk.ac.crc
Date: Tue, 19 Oct 1993 10:22:55 GMT
In article <1993Oct19.102319.24880 at gserv1.dl.ac.uk> Dr. M.F. Grahn,
mgrahn at uk.ac.crc writes:
>
>We are considering equipment from ABI ( model 373 ) or Pharmacia ALF
system.
>Any hidden costs, probllems, failures etc ? Any other choices, available
now,in 
>the offing? Any info. direct to me, and I will post results to the net.
Thas.
>
>Mike Grahn, London Hospital Medical College, UK



Tried to e-mail you, but for some reason it didnt go through......

Hi, I am a grad student in Dr. Dan Goldman's lab at the University of
Michigan.
 I saw and read your message and I'll give you some info on what we are
using
and how it is going.  We have the ABI model 373 in our lab.  We have had
it for
about 5 years.  I can say that we arent sequencing heavy in our lab, but
the
373 has been adequate for us.  About 4 years ago when I joined the lab we
were
having problems with the sequencing.  I believe that there were problems
with
the sequencing chemistries.  We just couldnt get any reliable sequence
with any
of our prepared plasmids.  (These usually were CsCl purified preps).  We
had
reps from ABI to come out and try to figure out what was going on and
they had
the same problems also.  

About a year ago we started to get more intensive in the sequencing and
suddenly the sequencing improved.  We dont know the reason, but I believe
that
ABI made modifications in the Amplitaq that we were using which made
sequencing
possible over wider variations in water purity, pH, and other conditions.
 We
also upgraded our PCR machine from an old COY model to the Perkin Elmer
9600. 
The 9600 works very well and I think has improved our sequencing data.  We
havent had much use of the Sequenase Kits, but the couple of times that we
tried it, it worked well.  With the Amplitaq procedure we are regularly
getting
sequencing from the primer up to 500 bases.  The sequencing reaction went
further than the 500 bases, but gel resolution is lost around this point.
 If
they could come up with a gel that would last longer, I believe we could
get
somewhere around 800 bases easily.  

About the only problems that we have been having recently is problems
with the
software provided.  We are running the data collection and analysis
programs on
a Macintosh IIcx using System 6 operating system.  The program that we are
using is a bare bones program which was made when the Mac IIs came out. 
The
problems we are having mostly occur at the analysis stage when at times,
the
analysis program will not automatically start, causing a delay in
obtaining
sequence.  The other problem centers around the data collection program
and the
features which are available.  We are very limited in the ability to
check a
currently running sequencing run with the software that we have right
now...

Most of the software problems may bee moot for you since ABI has come up
with
an upgrade for the Mac system 7 software.  This upgrade adds features and
I
believe speeds up the data collection itself.  I am not too familiar with
the
upgrades though.  We would probably be better off with the new upgrade,
but ABI
has put a price tag on the upgrade at $700.  Because we arent too
involved in
sequencing in the lab we are using the old software than dishing out the
$700
which is needed elsewhere. 

I'm sorry that I dont know anything about the other sequencing systems,
but I
hope that the info on the 373 has helped.  I have seen the advertisements
about
the ALF system and I am impressed with what they show, but of course
everything
in the magazines is always better than what you get....



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