Software to read SDS-PAGE

Robert Horton horton at biosci.cbs.umn.edu
Mon Dec 18 14:11:33 EST 1995


Dima Klenchin (klenchin at macc.wisc.edu) wrote:
: In article <dtyyu.148.0013AA4D at ucla.edu>,
:    dtyyu at ucla.edu (David Tak Yan Yu) wrote:
: >Is there a free software to calculate MW of proteins in SDS-PAGE?

: I don't get it. Do you need imaging program to be able to scan
: you gel and then digitize/edit it or you need to calculate MW?

: The latter does not require software: plot log(MW) vs distance
: and from this calibration curve (ideally,line) calculate 
: MW of you protein. There are many caveats discussed in many
: sources but software just can't help here. 

There are actually software programs that will fond the bands in an
image file, measure how far they migrated, and calculate MW
automatically.

One program for the Macintosh is called "GelReader" from NCSA. One
little hint; when we tried it, it required that you have standards at
both ends of the gel. This was not obvious from the documentation at the
time (I don't know if they've clarified that point yet).

You can download it from:
http://www.ncsa.uiuc.edu/SDG/Software/Brochure/MacSoftDesc.html

The file you choose depends on whether you have a floting point
co-processor or not.

This actually links you to
ftp://ftp.ncsa.uiuc.edu/Mac/GelReader/
(I put in the ftp address in case anybody has ftp access but not www. If
you're not familiar with this "URL" format for an ftp address, it means
you use ftp to the directory /Mac/GelReader/ of the server
ftp.ncsa.uiuc.edu).

Please let me know if you actually use the ftp address, rather than the
www site. If no one finds this useful, I won't bother to give both ways
in the future.

Here's more info copied from their web page:

===== Stuff from the NCSA GelReader for Macintosh Page follows: =====

SUMMARY:

NCSA GelReader is a color-imaging and analysis tool developed for
molecular biologists or others in need of electrophoretic gel
data analysis. The program extracts information from digitized
electrophoretic gel images such as DNA fragments. Allowing
interactive manipulation of lanes and bands, the tool helps
estimate the molecular weight of bands as well as generate
reports. NCSA GelReader was created with the assistance of UIUC's
Center for Prokaryotic Genome Analysis.

NCSA GelReader for the Macintosh: Overview

NCSA GelReader 2.0 is a software tool developed to help scientists
extract information from digitized electrophoretic gel images. It was
specifically designed for molecular biologists doing large-scale,
physical mapping, but its usefulness extends to other scientists
performing DNA, RNA and protein research as well.

Specifically, NCSA GelReader 2.0 employs the color-imaging capabilities
of the Macintosh to help the molecular biologist estimate the molecular
weights of electrophoretically separated DNA fragments.

[...]

Features 

NCSA GelReader 2.0 allows you to: 
	
	find the lanes in a gel image, semi-interactively

	add and delete lanes interactively

	find the bands (sites) in the image automatically add and delete
	bands interactively

	adjust the sensitivity of the band and lane searching algorithms

	create and modify standards that you can save as part of the program
	for subsequent use or use to assign standards to lanes and then
	discard

	create assay templates that you can save and reuse. These templates
	define the lane names, specify some lanes as standards, and
	designate what those standards are.

	generate reports of the molecular weights of the unknowns or their
	mobilities

	load gel images from TIFF, PICT, HDF or raw binary files

	save the results of the analysis into an HDF file along with the gel
	image

	view the profiles of the lanes in the same window with the gel

	superimpose standard lanes and bands copied from one image onto
	another using registration marks to identify the geometric
	relationship between the two images. This feature is useful if you
	are multiplexing Southern blots.

System Requirements

To use NCSA GelReader 2.0 you need a Macintosh with 256 color or
gray-scale capabilities, at least two megabytes of RAM and a monitor.
Additionaly, you will need to digitize the gels. The Hewlett Packard
ScanJet Plus 8-bit scanner is one mechanism that will allow you to do
this. Whatever the vehicle you use to digitize the gel, the gel image
file will have to be in a format (TIFF, PICT, HDF or raw binary files)
that the GelReader will be able to read.

======= Here Endeth the Stuff from the NCSA GelReader Page =======

Robert M. Horton (PhD!)         *CAUTION: .sig under construction*
U of M Dermatology Dept.
Box 98 UMHC, 4-154 PWB           (612)625-8941   http://134.84.47.3
Minneapolis, MN 55455       horton at biosci.cbs.umn.edu  Disclaimer:"Bob who?"





More information about the Methods mailing list