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Complexity Profiles of DNA Sequences Using Finite-Context Models

  • Armando J. Pinho
  • Diogo Pratas
  • Sara P. Garcia
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7058)

Abstract

Every data compression method assumes a certain model of the information source that produces the data. When we improve a data compression method, we are also improving the model of the source. This happens because, when the probability distribution of the assumed source model is closer to the true probability distribution of the source, a smaller relative entropy results and, therefore, fewer redundancy bits are required. This is why the importance of data compression goes beyond the usual goal of reducing the storage space or the transmission time of the information. In fact, in some situations, seeking better models is the main aim. In our view, this is the case for DNA sequence data. In this paper, we give hints on how finite-context (Markov) modeling may be used for DNA sequence analysis, through the construction of complexity profiles of the sequences. These profiles are able to unveil structures of the DNA, some of them with potential biological relevance.

Keywords

Complexity Measure Data Compression Kolmogorov Complexity Arithmetic Code Cyanidioschyzon Merolae 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Armando J. Pinho
    • 1
  • Diogo Pratas
    • 1
  • Sara P. Garcia
    • 1
  1. 1.Signal Processing Lab, IEETA / DETIUniversity of AveiroAveiroPortugal

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