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Nucleic Acids Research 2005 33(9):2806-2812; doi:10.1093/nar/gki580
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Published online 13 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Automated band mapping in electrophoretic gel images using background information

Troy Zerr and Steven Henikoff1,*

Basic Sciences Division, Fred Hutchinson Cancer Research Center Seattle, WA 98109, USA 1Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center Seattle, WA 98109, USA

*To whom correspondence should be addressed. Tel: +1 206 667 4515; Fax: +1 206 667 5889; Email: steveh{at}fhcrc.org

Received March 8, 2005. Revised April 13, 2005. Accepted April 27, 2005.

Some popular methods for polymorphism and mutation discovery involve ascertainment of novel bands by the examination of electrophoretic gel images. Although existing strategies for mapping bands work well for specific applications, such as DNA sequencing, these strategies are not well suited for novel band detection. Here, we describe a general strategy for band mapping that uses background banding patterns to facilitate lane calling and size calibration. We have implemented this strategy in GelBuddy, a user-friendly Java-based program for PC and Macintosh computers, which includes several utilities to assist discovery of mutations and polymorphisms. We demonstrate the use of GelBuddy in applications based on single-base mismatch cleavage of heteroduplexed PCR products. Use of software designed to facilitate novel band detection can significantly shorten the time needed for image analysis and data entry in a high-throughput setting. Furthermore, the interactive strategy implemented in GelBuddy has been successfully applied to DNA fingerprinting applications, such as AFLP. GelBuddy promises to make electrophoretic gel analysis a viable alternative to DNA resequencing for discovery of mutations and polymorphisms.


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