Scanning sequencing gels: Experiences?

Brain Foley brianf at
Tue Nov 9 16:23:55 EST 1993

Adam Richman (adam at wrote:
: I'd like to hear about others' experience with scanning sequencing gels,
: particularly set-ups for use with existing computers (Macs and others)
: since funds are limited.  I've heard of a system under development for
: Macs which uses a hand scanner, a color monitor, and software which
: identifies the lanes, (and allows the user to correct themif necessary),
: then displays the read sequence overlaid on the scanned image.  But I'd
: appreciate hearing about any approach which represents an advance over
: the use of a digitizing pen...

: Adam Richman

	It is not a scanner, and I'm sure that some would NOT consider it
an advance over a digitizing pen, but:
	I use SeqSpeak which is a hypercard stack that can be found in the
IUBIO archives.  It allows you to set up any order of sequencing lanes
(GATC or GTCA or CTGA etc) and you can then use four fingers on one hand
to type the sequence (the Mac speaks each letter as you type it) while
you use the other hand to keep track of where you are on the gel.
	Advantages of this program are that you can save you output in
several formats (GCG, Staden, GenBank etc), and that you can invert and
complement the sequence prior to export.
	I found that once I got my fingers coordinated, I could read up a
sequencing gel much faster with this than with a digitizing pen, and there
is no set-up required, you just put a light box near your keyboard, slap
your autorad down and start reading.  You don't have to define lanes, and
you don't have to worry about the computer miscalling bases (you can screw
it up  ;)  all by yourself).

*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *

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