Protein sequence analysis based on hydropathy profile of amino acids.

Biology sequence comparison is a fundamental task in computational biology. According to the hydropathy profile of amino acids, a protein sequence is taken as a string with three letters. Three curves of the new protein sequence were defined to describe the protein sequence.

[A new alignment-free sequence analysis based on the distribution of K-tuple].

Based on the distribution of K-tuple in complete genome, a method without doing sequence alignment to infer difference of biological sequence is proposed in this paper. The method can be used to measure the difference of distribution on K-tuple between the native DNA sequences and the corresponding randomized ones. Applied to construct phylogenetic trees of the complete mitochondrial genomes of 26 species of placental mammals, with K increasing, it yields phylogenetic trees of which the classification effect increasingly matches the result widely recognised by the biological field.

[Maximum entropy principle and population genetic equilibrium].

A general mathematic model of population genetic equilibrium was constructed based on the maximum entropy principle. We proved that the maximum entropy probability distribution was equivalent to the Hardy-Weinberg equilibrium law. A population reached genetic equilibrium when the genotype entropy of the population reached the maximal possible value.