Repeat Finding Techniques, Data Structures and Algorithms in DNA sequences: A Survey

Freeson Kaniwa, Heiko Schroeder, Otlhapile Dinakenyane

Abstract


DNA sequencing technologies keep getting faster and cheaper leading to massive availability of entire human genomes. This massive availability calls for better analysis tools with a potential to realize a shift from reactive to predictive medicine. The challenge remains, since the entire human genomes need more space and processing power than that can be offered by a standard Desktop PC for their analysis. A background of key concepts surrounding the area of DNA analysis is given and a review of selected prominent algorithms used in this area. The significance of this paper would be to survey the concepts surrounding DNA analysis so as to provide a deep rooted understanding and knowledge transfer regarding existing approaches for DNA analysis using Burrows-Wheeler transform, Wavelet tree and their respective strengths and weaknesses. Consequent to this survey, the paper attempts to provide some directions for future research.

Keywords


DNA sequences; Repeats; Burrows-Wheeler transform; Wavelet trees

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