DNA Repeats Detection Using a Dedicated Dot-Plot Analysis

Gavril Petre Pop

Abstract


DNA repeats are believed to play significant roles in genome evolution and diseases. Many of the methods for finding repeated sequences are part of the digital signal processing (DSP) field and most of these methods use distances, similarities and consensus sequences to generate candidate sequences. This paper presents results obtained using a dedicated numerical representation with a mapping algorithm (using  DNA distances and consensus types) and a custom dot-plot analysis (using similarities to represent DNA patterns) combined with image processing techniques, to visual isolate the position of DNA patterns with different lengths. The final images that best put in evidence the presence of repeated sequences were obtained using weighted cosine cross-correlation, Jukes-Cantor distance and Motyka similarity.


Full Text:

PDF

References


K. G. Lim, C. K. Kwoh, L. Y. Hsu, A. Wirawan, "Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance," Brief Bioinform., vol. 14, no. 1, pp. 67-81, Jan. 2013.

M. K. Rudd, G. A. Wray, H. F. Willard, The evolutionary dynamics of a-satellite, Genome Res, 16:88-96, 2006.

J. V. Lorenzo-Ginori, A. Rodriguez-Fuentes, R. G. Abalo, R. S. Rodrigues, "Digital signal processing in the analysis of genomic sequences," Curr. Bioinformatics, vol. 4, pp. 28-40, 2009.

P. G. Pop, A. Voina, "Numerical Representations Involved in DNA Repeats Detection Using Spectral Analysis," Studies in Informatics and Control, vol. 20, no. 2, pp. 163-180, 2011.

D. Yankov, E. Keogh, S. Lonardi, "Dot plots for time series analysis," Proc. 17th IEEE Int. Conf. on Tools with Artificial Intelligence, pp. 159-168, 2005.

C. Sung-Hyuk, "Comprehensive Survey on Distance/Similarity Measures between Probability Density Functions," Int. J. of Mathematical Models and Methods in Applied Sciences, vol. 1, no. 2, pp. 300-307, 2007.

T. D. Schneider, "Consensus Sequence Zen," Applied Bioinformatics, vol. 1, no. 3, pp: 111-119, 2002.

N. Hamadani, "Automatic target cueing in IR imagery", Master Thesis, Air Force Institute of Technology, -WPAFB. Ohio.

C. Alkan, M. Ventura, N. Archidiacono, M. Rocchi, S. C. Sahinalp, E. E. Eichler, "Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data," PLoS Comput Biol., vol. 3, no. 9, pp. 1807-1818, Sep. 2007.

V. Paar, N. Pavin, I. Basar, M. Rosandic, M. Gluncic, N. Paar, Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats, BMC Bioinformatics, vol. 9, no. 1, 466, 2008.




DOI: http://dx.doi.org/10.11601/ijates.v4i3.140

Refbacks

  • There are currently no refbacks.