Abstract
This paper presents a top-down strategy to detect features in genomic sequences. The strategy's core is to exploit dictionary-based compression algorithms and analyse the content of the automatically generated dictionary. We classify the different over-represented segments and in the case study we correlate them to experimentally identified or theoretically forecasted biological features. A large spectrum analysis reveals that the only feature co-located with the a priori extracted segments is the torsional flexibility of DNA, while non-B DNA configurations are anti-localized and other features are mostly independent of the extracted sequences. This analysis unravels complex relationships between the linguistic structures investigated under our approach and some known biological features.
Original language | English |
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Pages (from-to) | 134-142 |
Number of pages | 9 |
Journal | Journal of Theoretical Biology |
Volume | 270 |
Issue number | 1 |
DOIs | |
Publication status | Published - Feb 7 2011 |
Keywords
- Combinatorics on words
- DNA flexibility
- Over-represented segments
ASJC Scopus subject areas
- Medicine(all)
- Immunology and Microbiology(all)
- Biochemistry, Genetics and Molecular Biology(all)
- Agricultural and Biological Sciences(all)
- Modelling and Simulation
- Statistics and Probability
- Applied Mathematics