I am looking for a system for automating entry of sequence
data into the computer in our lab.
We are a midsized (about 12 of us) biochemistry lab who
sequence 2-10 kb per year to verify clones and site directed
mutants. We use Sanger di-deoxy sequencing with Sequenase and
35-S-dATP on acrylamide gels and X-ray film. We use an IBM clone
(386-25) and GCG on a VAX for sequence analysis.
Currently we read sequence films on a light box, record data
on scratch paper, and type it into the computer for analysis.
This is tedious and error prone.
The lab PI recently asked me to recommend a system to enter
sequence data into the computer automatically. He wants to spend
under $1,000- and wants to stick to the traditional autorad
technology that he feels comfortable with.
I have a vision of a system in mind, but have no idea if
anything like it exists. I envision a small scanner device to
enter data into the computer and software which would allow you
to see the autorad on screen. I would like to see a visual
picture of the computers choices for reading the sequence which
could be edited on screen by the user. Data should be in a
format which could be easily saved as an ASCII file of sequence
or directly shipped down to the vax for GCG to analyze.
Ideally, I would like some versatility in the system. If I
had a scanner on hand, I would like to be able to use it to enter
sequence from old publications or faxed data directly from text
on paper. I would like the option to digitize pictures of
agarose gels into the computer to use graphics programs to add
pointers and text to the gel picture for publication quality
This system would require some hardware and some software,
of which we have neither. The last system I used was purchased
around 1986 and I no longer have access to it or any of it's
components. Any suggestions for hardware and/or software for a
system like this would be greatly appreciated. In leu of my
dream system, I would also appreciate any recommendations from
people using small scale automated sequence data entry systems.
Any warnings or advice will be greatly appreciated.
A summary will be posted back to the net if I get anything
interesting and helpful back. If I get nothing I will try
posting to autoseqs, but I don't subscribe to that group.
Dr. Leonard N. Bloksberg
PreissJ at clvax1.cl.msu.edu
Dept. of Biochemistry
Michigan State University
"Life is weird"