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Biomedical subjects

A N Gorban'

Publications and source records attributed to A N Gorban'.

11 recordsLinked to original sources
PubMed1996

[Genes of human viruses are less redundant than human genes].

Statistical parameters of nucleotide sequences of mature human RNAs and those of human viruses were compared. The redundancy values of the appropriate genes were compared. The redundancy of virus genes was shown to be, on the average, less than that of human genes. The distribution of human genes according to redundancy values is bimodal, and that of human virus genes is trimodal. This fact suggests possibility of a novel gene classification according to statistical characteristics of nucleotide sequences.

Data Interpretation, Statistical↗
PubMed1993

[Comparative redundancy of genes of various organisms and viruses].

This paper is devoted to the comparative study of redundancy of genetic texts of various organisms and viruses. To determine the redundance of a gene, we have introduced the strict measure for that latter. The measure for a text's redundance is the length of restriction of Frequency/Correlation Dictionary of a given genetic text. Frequency/Correlation Dictionary is the ser of all subsequences belong to a given genetic text, accompanied by the frequencies of their occurrence. The restriction length is defined as that one, for which all the subsequences (of that length) are unique. We have found, that genes of human viruses are less redundant, in comparison to those of human genes. Other aspects of a comparative redundance investigations of the genes are discussed. The problem of the determination of "truet" intron could be treated by this methodology, as well, as the evolution of genome.

Amino Acid Sequence↗
PubMedDate not supplied

[Classification of nucleotide sequences over their frequency dictionaries reveals a relation between the structure of sequences and taxonomy of their bearers].

Classification of 16S RNA sequences over their frequency dictionaries, both real ones, and transformed ones was studied. Two entities were considered to be close each other from the point of view of their structure, if their frequency dictionaries were close, in Eucledian metric. A transformation procedure of a frequency dictionary has been implemented that reveals the peculiarities of information structure of a nucleotide sequence. A comparative study of two classification developed over the real frequency dictionary vs. that one developed over the transformed frequency dictionary was carried out. The strong correlation is revealed between the classification and the taxonomy of 16S RNA bearer. For the classes isolated, the information valuable words were identified. These words are the main factors of a difference between the classes. The frequency dictionaries containing the words of the length 3 exhibit the best correlation between a class and a genus. A genus, as a rule, is included into the same class, and the exclusion are sporadic. A development of hierarchy classification over the transformed frequency dictionaries separated one or two taxonomy groups, as each stage of classification. The unexpectedly frequent, or contrary, unexpectedly rare occurred of words (of the length 3) in entities under consideration make the structure difference between the classes of the nucleotide sequences.

Bacteria↗
PubMedDate not supplied

[Optimal strategies of spatial distribution: the Olli effect].

The selection of strategies of spatial distribution of individuals has been studied. In case of non-monotonous dependence of reproduction coefficient on the mean population density, a cluster formation is possible. At low mean densities, parity strategies of spatial distribution are realized, and at high densities, non-parity ones. A generalized notion of parity strategy of spatial distribution has been proposed. It includes such expenditures as expenditure for the movement of an individual, defense of the territory etc. A problem of evolutionary stability of different strategies of spatial distribution has been discussed.

Animals↗
PubMedDate not supplied

[A correlational approach to the comparison of nucleotide sequences].

A new method of evaluation of similarity between two nucleotide sequences is proposed. It is based on comparing frequency/correlation dictionaries of the sequences under investigation. The dictionary is a set of all strings of various length occurring within the sequences accompanied by their frequencies. The method proposed allows to compare sequences of arbitrary lengths, its advantage is absence of necessity of informal (expert) choice of the best fit. Efficiency of the method is demonstrated by comparison of several human genes and viruses.

Base Sequence↗
PubMedDate not supplied

[Redundancy of genetic sequences and mosaic structure of a genome].

A new method is developed to measure and compare the redundancy of genes. The method is based on the creating a Frequency/Correlation Dictionary of a gene. The Dictionary is a set of all possible words (i.e., subsequences) which could be met within a gene, of a length from 1 to N, where N is the length of the gene. The measure of redundancy of a gene is the minimal length of words which occur in the gene as a single copy. The results of the redundancy measurements are presented in the paper. It is shown that genes are not homogeneous in respect of redundancy of various sites in the gene. This phenomenon was called a mosaic pattern.

Genome, Human↗
PubMedDate not supplied

[A new approach to the study of statistical properties of genetic sequences].

An approach to the study of the properties of genetic texts is proposed. It is based on the investigation of the frequencies of all possible words (subsequences) in a text. The most important effect is that the original text could be reconstructed completely without deletions and/or mistakes using the set of words which are met in the text as a single copy. The length of words for which the effect occurs is a measure of the text redundancy. Some real genetic sequences were studied as well.

Humans↗
PubMedDate not supplied

[Information capacity of the nucleotide sequences and their fragments].

The problem of determining the information content of nucleotide sequences is discussed. Exact expressions for the reconstitution of higher-order frequency dictionaries from lower-order once were obtained by the maximum entropy method. In form, they are analogous to superpositional approximations known in statistical physics. The features of entropy characteristics of real nucleotide sequences are described that reliably distinguish them from random texts. Methods for comparing the information content of frequency dictionaries and assessing the residual uncertainty of the text at the known frequency dictionary are proposed.

Base Sequence↗