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Каталог книг и продолжающихся изданий библиотеки Института биофизики СО РАН (75)

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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorban' A.N., Mirkes Ye.M., Popova T.G., Sadovskii M.G.
Заглавие : A new approach to the study of the statistical properties of gene sequences
Место публикации : Biophysics. - 1993. - Vol. 38, Is. 5. - P783-787. - ISSN 00063509 (ISSN)
Аннотация: An essentially new method is proposed for studying the statistical properties of gene sequences (g.s.) based on construction of a frequency-correlation dictionary (f.c.d.) for the g.s. being investigated (the f.c.d. is the set of all subsequences (words) with a length from 1 to N together with the frequencies of their encounter in the g.s. studied). It is shown that a measure of the redundancy of the g.s. is the characteristic length of the word d* starting from which all the words in the g.s. are unique, i.e. have the frequency 1. В© 1994.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Sadovsky M.G.
Заглавие : Comparison of real frequencies of strings vs. the expected ones reveals the information capacity of macromoleculae
Колич.характеристики :16 с
Место публикации : J. Biol. Phys.: SPRINGER, 2003. - Vol. 29, Is. 1. - P23-38. - ISSN 0092-0606, DOI 10.1023/A:1022554613105
Примечания : Cited References: 45
Предметные рубрики: DNA-SEQUENCE
ENTROPY
REDUNDANCY
Ключевые слова (''Своб.индексиров.''): dictionary--entropy--information capacity--markov model--ordered sequence--random sequence--reconstructed dictionary--specific entropy
Аннотация: The information capacity of nucleotide sequences is defined through the calculation of specific entropy of their frequency dictionary. The specific entropy of the frequency dictionary is calculated against the reconstructed dictionary; this latter bears the most probable continuations of the shorter strings. This developed measure allows to distinguish the sequences both from the randons ones, and from those with high level of (rather simple) order. Some implications of the developed methodology in the fields of genetics, bioinformatics, and molecular biology are discussed.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Sadovsky M.G.
Заглавие : Comparison of symbol sequences: No editing, no alignment
Колич.характеристики :18 с
Место публикации : Open Syst. Inf. Dyn.: KLUWER ACADEMIC PUBL, 2002. - Vol. 9, Is. 1. - P19-36. - ISSN 1230-1612, DOI 10.1023/A:1014278811727
Примечания : Cited References: 12
Предметные рубрики: MULTIPLE
Аннотация: The new method to compare two (or several) symbol sequences is developed. The method is based on the comparison of the frequencies of the small fragments of the compared sequences; it requires no string editing or other transformations of the compared objects. The comparison is provided through a calculation of the specific entropy of a frequency dictionary against the special dictionary called the hybrid one; the latter is the statistical ancestor of the group of sequences to be compared. Some applications of the method developed to genetics, bioinformatics, and linguistics axe discussed.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : GORBAN A.N., POPOVA T.G., SADOVSKY M.G.
Заглавие : CORRELATION APPROACH TO COMPARING NUCLEOTIDE-SEQUENCES
Колич.характеристики :11 с
Место публикации : Zhurnal Obshchei Biol.: MEZHDUNARODNAYA KNIGA, 1994. - Vol. 55, Is. 04.05.2013. - P420-430. - ISSN 0044-4596
Примечания : Cited References: 22
Аннотация: 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.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Gorbunova E.O., Kondratenko Y.V., Sadovsky M.G.
Заглавие : Data loss reparation due to indeterminate fine-grained parallel computation
Колич.характеристики :8 с
Место публикации : COMPUTATIONAL SCIENCE - ICCS 2003, PT II, PROCEEDINGS. Ser. LECTURE NOTES IN COMPUTER SCIENCE: SPRINGER-VERLAG BERLIN, 2003. - Vol. 2658: International Conference on Computational Science (ICCS 2003) (JUN 02-04, 2003, MELBOURNE, AUSTRALIA). - P794-801. - ISBN 0302-9743. - ISBN 3-540-40195-4
Примечания : Cited References: 6
Аннотация: The new method of a gap recovery in symbol sequences is presented. A covering is combined from the suitable reasonably short strings of the parts of a sequence available for an observation. Two criteria are introduced to choose the best covering. It must yield the maximum of entropy of a frequency dictionary developed over the sequence obtained due to the recovery, if an overlapping combined from the copies of strings from the available parts of the sequence exists. The second criterion identifies the best covering in case when one has to use any string to cover the gap; here the best covering must yield the minimum of specific entropy of the frequency dictionary developed over the available parts of the sequence against that one developed over the entire sequence obtained due to the recovery. Kirdin kinetic machine that is the ideal fine-grained structureless computer has been used to resolve the problem of the reconstruction of a gap in symbol sequence.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kirsanova E.N., Sadovsky M.G.
Заглавие : Entropy approach to comparison of images
Колич.характеристики :17 с
Место публикации : Open Syst. Inf. Dyn.: KLUWER ACADEMIC PUBL, 2001. - Vol. 8, Is. 2. - P183-199. - ISSN 1230-1612, DOI 10.1023/A:1011962818766
Примечания : Cited References: 10
Аннотация: Basically new pattern recognition method is implemented to compare two (or several) digital images. The method has neither feature alphabet, nor pattern dictionary recovery stages. It compares input images due to a special object called palette built from fragments of images. The measures to estimate the distances between images are based on a determination of the specific entropy of the frequency dictionary of all image with respect to the palettes that latter presents the statistical ancestor of the group of the images under comparison. The palette is defined as the frequency dictionary with frequencies of the fragments equal to arithmetic mean of the frequencies of the same fragments from the images to be compared. Such definition yields a minimum of the sum of specific entropies of the compared images with respect to the palette. Some preliminary results in the application of the method in pattern recognition and synergistics problems are presented. The limitations and basic properties of the method are discussed.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Nemenchinskaya E.O., Kondratenko Y.V., Sadovsky M.G.
Заглавие : Entropy based approach to data loss reparation through the indeterminate fine-grained parallel computation
Колич.характеристики :15 с
Место публикации : Open Syst. Inf. Dyn.: KLUWER ACADEMIC PUBL, 2004. - Vol. 11, Is. 2. - P161-175. - ISSN 1230-1612, DOI 10.1023/B:OPSY.0000034194.24443.22
Примечания : Cited References: 27
Предметные рубрики: IMAGE SEQUENCES
MISSING DATA
RECOVERY
Аннотация: The new method of a gap recovery in symbol sequences is presented. A covering is combined from the suitable reasonably short strings of the parts of a sequence available for observation. Two criteria are introduced to choose the best covering. It must yield the maximum of entropy of a frequency dictionary developed over the sequence obtained due to the recovery, if an overlapping combined from the copies of strings from the available parts of the sequence exists. The second criterion identifies the best covering in case when one has to use any string to cover the gap; here the best covering must yield the minimum of specific entropy of the frequency dictionary developed over the available parts of the sequence against the one developed over the entire sequence obtained due to the recovery. Kirdin kinetic machine which is the ideal fine-grained structureless computer has been used to resolve the problem of the reconstruction of a gap in symbol sequence.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Sadovsky M.G.
Заглавие : Information capacity of symbol sequences
Колич.характеристики :13 с
Место публикации : Open Syst. Inf. Dyn.: KLUWER ACADEMIC PUBL, 2002. - Vol. 9, Is. 1. - P37-49. - ISSN 1230-1612, DOI 10.1023/A:1014230928565
Примечания : Cited References: 23
Предметные рубрики: REDUNDANCY
INTRONS
Аннотация: The information capacity of sequences is considered through the calculation of specific entropy of their frequency dictionary. The specific entropy was calculated against the reconstructed dictionary which bears the most probable continuations of shorter strings. The measure developed allows to distinguish the sequences both from the random ones, and those with high level of (rather simple) order. Some applications of the developed methodology to genetics, bioinformatics, and linguistics axe discussed.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Sadovsky M.G.
Заглавие : On the problem of genome redundancy in viruses and prokaryotes
Колич.характеристики :7 с
Место публикации : Russ. J. Genet.: KLUWER ACADEMIC/PLENUM PUBL, 2002. - Vol. 38, Is. 5. - P575-581. - ISSN 1022-7954, DOI 10.1023/A:1015503617023
Примечания : Cited References: 10
Аннотация: A specific index of nucleotide sequence redundancy, the specific restriction length of a finite frequency dictionary, was determined for a complete set of genes in some viral genomes and a genome of a bacterium, Bacillus subtilis. The distribution of the gene number over the specific restriction length was shown to be bimodal for viral genomes and unimodal for the Bac. subtilis genome. These results agree with earlier data.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : GORBAN A.N., POPOVA T.G., SADOVSKII M.G.
Заглавие : REDUNDANCY OF GENETIC TEXTS
Колич.характеристики :8 с
Место публикации : Mol. Biol.: PLENUM PUBL CORP, 1994. - Vol. 28, Is. 2. - P206-213. - ISSN 0026-8933
Примечания : Cited References: 14
Ключевые слова (''Своб.индексиров.''): gene--correlation--redundancy
Аннотация: A new method is proposed for measuring and comparing the redundancy of genetic texts. It is based on compiling for a given text a frequency/correlation dictionary encompassing all the words (subsequences) of length from 1 to N encountered in the text (N is text length); the measure of redundancy is the minimal length at which all words are unique. Preliminary results are reported for different genetic texts.
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11.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : GORBAN A.N., MIRKES E.M., POPOVA T.G., SADOVSKY M.G.
Заглавие : THE COMPARATIVE REDUNDANCY OF GENES OF VARIOUS ORGANISMS AND VIRUSES
Колич.характеристики :7 с
Место публикации : Genetika: MEZHDUNARODNAYA KNIGA, 1993. - Vol. 29, Is. 9. - P1413-1419. - ISSN 0016-6758
Примечания : Cited References: 20
Предметные рубрики: CODON
Аннотация: This paper is devoted to the comparative stude of redundancy of genetic texts of various organisms and viruses. To determine the tedundance 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 Frequence/Correlation Dictionary of a given genetic text. Frequence/Correlation Dictionary is the ser of all subsequences belang 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 invastigations 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.
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12.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Sadovsky M.G.
Заглавие : The method to compare nucleotide sequences based on the minimum entropy principle
Колич.характеристики :14 с
Место публикации : Bull. Math. Biol.: ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD, 2003. - Vol. 65, Is. 2. - P309-322. - ISSN 0092-8240, DOI 10.1016/S0092-8240(02)00107-6
Примечания : Cited References: 20
Предметные рубрики: GENOME
Аннотация: A new method to compare two (or several) symbol sequences is developed. The method is based on the comparison of the frequencies of the small fragments of the compared sequences; it requires neither string editing, nor other transformations of the compared objects. The comparison is executed through a calculation of the specific entropy of a frequency dictionary against the special dictionary called the hybrid one; this latter is the statistical ancestor of the group of sequences under comparison. Some applications of the developed method in the fields of genetics and bioinformatics are discussed. (C) 2003 Society for Mathematical Biology. Published by Elsevier Science Ltd. All rights reserved.
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