ABSTRACT
To describe the fractal feature of CGR (Chaos-game representation) graph of genomes sequences, a multifractal theory is presented in the analysis. By studying the effect of three probability sets on the scale invariance range, the probability set with the best scale invariance is chosen, and then the smooth general dimension spectrum and multifractal spectrum are calculated. The experimental result shows that the probability set composed of the relative probability has the best scale-invariance performance. The scale invariance has three different variance regions, which indicate that genomes sequence segments with different lengths have different distribution rules. It is concluded that the multifractal method is effective for describing the fractal feature of CGR graph of genomes sequences.
Subject(s)
Humans , Algorithms , Base Sequence , Computer Simulation , Game Theory , Genome , Mathematical Computing , Sequence Analysis, DNAABSTRACT
Biosequence analysis is the primary research field of bioinformatics. In this field, useful information can be extracted by comparison analysis methods. Among them, sequence alignment is the most common comparison method. However the sequence comparison by alignment, which assumes conservation of contiguity between homologous segments, is at odds with genetic recombination. Especially for the multisequence alignment, there exists the difficulty in the complexity of calculation. Therefore, alignment-free sequence comparison methods are required. In this paper, two main categories of alignment-free sequence comparison methods are reviewed. The first one is based on the word (oligomer) frequency and its distribution. The sequences are compared using the distances defined in a Cartesian space by the frequency vectors. In the second category, sequences are compared using Kolmogorov complexity and chaos theory.