Self-similarity in DNA sequences

Characterizing self-similarity in bacteria DNA sequences

YASS: Similarity search in DNA sequences

We describe YASS – a new tool for finding local similarities in DNA sequences. The YASS algorithm first scans the sequence(s) and creates on the fly groups of seeds (small exact repeats obtained by hashing) according to statistically-founded criteria. Then it tries to extend those groups into similarity regions on the basis of a new extension criterion. The method can be seen as a compromise be...

Arithmetic Self-Similarity of Infinite Sequences

We define the arithmetic self-similarity (AS) of a one-sided infinite sequence σ to be the set of arithmetic subsequences of σ which are a vertical shift of σ. We study the AS of several families of sequences, viz. completely additive sequences, Toeplitz words and Keane’s generalized Morse sequences. We give a complete characterization of the AS of completely additive sequences, and classify th...

Self-similarity and finite-time intermittent effects in turbulent sequences

We discuss two questions related to the finite-time behaviour of a sequence that generates a self-similar system. The first one concerns the way to approach the self-similarity exponent associated with the system, from the analysis of the sequences observed during a finite time. After this approximation procedure we established a criterion to decide whether the analysed sequence can be consider...

Self-similarity and Nite Time Intermittent Eeects in Turbulent Sequences

We propose a method to analyze a turbulent sequence focusing on the self-similar properties of the discrete system it generates. First we show how to approximate the self-similar exponent (= 1=3 in the case of hydrodynamic turbulence) from the nite time measurements, and then we establish a criterion to characterize the deviations from asymptotic scaling of the empirical measure generated by ni...