Sequencing survey

David Mathog mathog at seqvax.caltech.edu
Thu Aug 13 20:18:00 EST 1992


We're thinking about setting up a sequencing facility for the division and
are now in the process of collecting feedback from people who have
experience in this area.  If the shoe fits, please take a few minutes to fill
out this questionnaire, if not, no need to reply.

Thanks in advance for your time,

David Mathog
mathog at seqvax.caltech.edu
manager, sequence analysis facility, biology division, Caltech




Background:

We currently have a central facility for analyzing sequence, but no
equivalent facility for generating it.  We would like to provide a
sequencing service that works something like this: 

 LAB ->  $$$ + DNA  -> Facility (shortest time possible) -> Sequence -+
  ^                                                                   |
  |                                                                   |
  +-------------------------------------------------------------------+

Each lab would do its own DNA preps, but all of the actual sequencing
reactions and reading of the sequences would be done by the central 
facility.  The final sequences would be deposited directly into the
end users' directories on our sequence analysis facility's computer.

A survey of the division indicated that roughly 2500 sequencing
(radioactive) gels are run each year. 



Questions:

1.  What has been your experience (positive and negative) with the 
various commercially available fluorescent sequencers?

2.  Which of the various types of fluorescent sequencing reactions 
have you tried and how well have they worked?

3a.  Assuming that the incoming DNA just needs to be pipetted into the
sequencing reactions how much manpower are we going to need to handle the
expected workload? 

3b.  How many machines will it require?

3c.  We'd like to turn around the average job in a day or less, is
this a reasonable goal?  What sort of schedule do you run?  How much 
do you charge/sequencing reaction (if you charge)?

4.  What software do you use to analyze the traces, how well does 
it work, and what does it cost?

5. If you've got the numbers - what does it REALLY cost you to
convert a single DNA sample to sequence?  If possible, break it down
reagents/overhead/labor/machinery/etc.  Also, if you've got the
numbers, what did it used to cost you to sequence with 35-S/32-P?  (We
will need at least an estimate of these numbers to justify the expense
of setting up the facility). 

6. If you ever used one of the commercial sequencing services how much
did it cost, what was their turn around time, and were you pleased
with the results? 

7.  If _you_ were going to set up a facility like this, how would you do 
it?

8.  Any other comments or suggestions?

Thank you for filling out the form!




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