New Software for gel image processing

Joaquin Dopazo dopazo at samba.cnb.uam.es
Thu Jun 22 14:52:22 EST 1995


GEL MANAGER 1.1

A Program For the Analysis of Electrophoretic 1D Gels


Developed at :
Centro Nacional de Biotecnología, CSIC. Universidad Autónoma, Madrid, SPAIN
Under a contract of  TDI SA
Authors: Carlos Vaquerizo and Joaquín Dopazo


The program
   We present a new concept in the field of comparison and analysis of electrophoretic 
profiles. Gel Manager is a user friendly program which runs in Microsoft Windows 
environment. It includes advanced techniques of image processing along with sophisticated 
options for data  analysis. It can deal with different kinds of data such as: RFLP, RAMM, 
RAPD, microsatellites and other fingerprinting techniques. Their capacities of data 
processing make of Gel Manager a multipurpose program extremely useful for many types 
of studies including the definition of genetic relationships, taxonomy and classification , 
epidemiology, etc. 


Image processing

   Using the digitalized image of a gel or a film, Gel Manager performs a cleaning of the 
image removing noise by means of different advanced methods of image processing. Images 
can be retrieved in many standard graphic formats (BMP, PCX, TIFF, etc.). Next, the 
program automatically finds the positions of the bands of every lane, by means of a high 
precision algorithm, and estimates their molecular weights using as reference any marker of 
electrophoretic migration. Every selected lane is presented as a profile of intensity with the 
detected bands marked. The program provides a series of tools to manually define, remove 
or move peaks. The threshold of detection is very easy to use and can be changed to detect 
very weak bands over a noisy background. Distortion in gels can be easily corrected by 
defining base lines which allows the recalculation of the positions of every band by 
interpolation. Each image with all the operations performed over it can be stored as a 
session which can be reloaded later. On the other hand, all the molecular weights obtained 
can be stored in databases which allow to perform different comparisons between the lanes.

Data analysis

   Considering the most recent scientific literature, Gel manager provides different indexes 
appropriate for the comparison of samples studied by means of different techniques. Results 
of the comparisons can be displayed as a divergence matrix or as a dendrogram, obtained 
by the UPGMA method.


   All these characteristics set to Gel Manager among the most advanced software in the 
field of digital analysis of electrophoretic gels for PC computers.

AVAILABILITY

Have a look to gel manager in our Web page at the URL:
HTTP://WWW.CNB.UAM.ES/WWW/PROGRAMAS/GEL_MAN/GM.HTML
You can retrieve a DEMO copy in out FTP at the internet address:
FTP.CNB.UAM.ES
in the directory SOFTWARE/MOLBIOL
Alternatively you can send your requests to 100626.13 at compuserve.com

You are kindly invited to visit our Software Web page at the URL:
HTTP://WWW.CNB.UAM.ES/www/programas/pag-soft.html






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