A relative Lempel–Ziv complexity: Application to comparing biological sequences

Comparing complexity classes relative to physical oracles

We develop the idea of using a physical experiment as an oracle to an algorithm. As a case study, we compare the computational power of deterministic and non-deterministic Turing machines connected to a simple physical oracle, namely, the scatter machine experiment. We prove relativisation theorems for the conjectures concerning P , NP , PSPACE relative to this physical oracle. Finally, we refl...

Strings Processing and Application to Biological Sequences

Finite Inductive Sequences, Kolmogorov Complexity with Application to Genome Sequences

We describe current work in examining the complexity of genomic sequences at the amino acid level. We have provided an original algorithm description and research results when considering this algorithm as a measure of Kolmogorov complexity of such candidate strings. The results can be used to estimate comparative string values, identifying substrings with comparable values, and determining reg...

A computational method to analyze the similarity of biological sequences under uncertainty

In this paper, we propose a new method to analyze the difference and similarity of biological sequences, based on the fuzzy sets theory. Considering the sequence order and some chemical and structural properties, we present a computational method to cluster the biological sequences. By some examples, we show that the new method is relatively easy and we are able to compare the sequences of arbi...

On Reducing sequences and an Application to Local Cohomology Modules