GelJ – a tool for analyzing DNA fingerprint gel images

BMC Bioinformatics

Software

Carmen Lozano¹  Carmen Torres¹  Myriam Zarazaga¹  Vico Pascual²  Jónathan Heras²  César Domínguez²  Eloy Mata² 

[1] Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, 26006, Logroño, Spain;Department of Mathematics and Computer Science, University of La Rioja, Ed. Vives. C/ Luís de Ulloa 2, 26004, Logroño, Spain;

关键词: DNA fingerprinting;    Image analysis;    Clustering;    Java;    Database;   

DOI  :  10.1186/s12859-015-0703-0

 received in 2015-04-28, accepted in 2015-08-13,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundDNA fingerprinting is a technique for comparing DNA patterns that has applications in a wide variety of contexts. Several commercial and freely-available tools can be used to analyze DNA fingerprint gel images; however, commercial tools are expensive and usually difficult to use; and, free tools support the basic functionality for DNA fingerprint analysis, but lack some instrumental features to obtain accurate results.ResultsIn this paper, we present GelJ, a feather-weight, user-friendly, platform-independent, open-source and free tool for analyzing DNA fingerprint gel images. Some of the outstanding features of GelJ are mechanisms for accurate lane- and band-detection, several options for computing migration models, a number of band- and curve-based similarity methods, different techniques for generating dendrograms, comparison of banding patterns from different experiments, and database support.ConclusionsGelJ is an easy to use tool for analyzing DNA fingerprint gel images. It combines the best characteristics of both free and commercial tools: GelJ is light and simple to use (as free programs), but it also includes the necessary features to obtain precise results (as commercial programs). In addition, GelJ incorporates new functionality that is not supported by any other tool.

【 授权许可】

CC BY   
© Heras et al. 2015