GelJ – a tool for analyzing DNA fingerprint gel images

BMC Bioinformatics

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

[1] Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño 26006, Spain

[2] Department of Mathematics and Computer Science, University of La Rioja, Ed. Vives. C/ Luís de Ulloa 2, Logroño 26004, Spain

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

Others  :  1229481
DOI  :  10.1186/s12859-015-0703-0

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

【 摘 要 】

Background

DNA 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.

Results

In 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.

Conclusions

GelJ 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】

   
2015 Heras et al.

【 图 表 】

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

【 参考文献 】

• [1]Trends in DNA Fingerprint Research. Nova Science Publishers, Inc, New York, USA; 2005.
• [2]Heras J, Domínguez C, Mata E, Pascual V, Lozano C, Torres C, et al. A Survey of Tools for Analysing DNA Fingerprints. Brief Bioinform. 2015. doi:10.1093/bib/bbv016.
• [3]Schneider CA, Rasband WS, Eliceiri KW. NIH Image to ImageJ. Nat Methods. 2012; 9:671-5.
• [4]Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten I. The weka data mining software: An update. SIGKDD Explorations. 2009; 11(1):10-18.
• [5]Oracle. JavaDB Reference Manual. Technical report. 2014. http://www. oracle.com/technetwork/java/javadb/overview/index.html webcite
• [6]Sternberg SR. Biomedical Image Processing. Computer. 1983; 16(1):22-34.
• [7]Vauterin L, Vauterin P. Integrated Databasing and Analysis. Molecular Identification, Systematics, and Population Structure of Prokaryotes. Stackebrandt E, editor. Springer, Germany; 2006.
• [8]Ismail I, Eltaweel GS, Nassar H. Bands detection and Lanes segmentation in DNA Fingerprint images. J Inf Comput Sci. 2014; 9(4):243-51.
• [9]Skutkova H, Vitek M, Krizkova S, Provazník I. Preprocessing and Classification of Electrophoresis Gel Images Using Dynamic Time Warping. Int J Electrochemical Sci. 2013; 8:1609-1622.
• [10]Anderberg MR. Cluster Analysis for Applications. Academic Press, New York, USA; 1973.
• [11]Hassan WM, Wang SY, Ellender RD. Methods To Increase Fidelity of Repetitive Extragenic Palindromic PCR Fingerprint-Based Bacterial Source Tracking Efforts. Appl Environ Microbiol. 2005; 71(1):512-8.
• [12]Applied Maths NV. GelCompar II version 6.6.11. 2013. http://www. applied-maths.com webcite
• [13]DNR Bio-Imaging Systems Ltd. GelQuant Pro version 13. 2013. http://www. dnr-is.com/Product.asp?Par=3.19&id=81 webcite
• [14]GE Healthcare Life Sciences. ImageQuant TL 7.0. 2010. http://www. gelifesciences.com/ webcite
• [15]TotalLab Limited. Phoretix 1D Pro version 11.4. 2013. http://totallab. com/cliqs-1d-pro/ webcite
• [16]TotalLab Limited. TotalLab Quant version 13. 2013. http://totallab. com/cliqs/ webcite
• [17]Khakabimamaghani S, Najafi A, Ranjbar R, Raam M. GelClust: A software tool for gel electrophoresis images analysis and dendrogram generation. Comput Methods Programs Biomed. 2013; 111(2):512-8.
• [18]Pavel A, Vasile C. PyElph – a software tool for gel images analysis and phylogenetics. BMC Bioinform. 2012;13(9). doi:10.1186/1471-2105-13-9.