BOX COUNTING METHOD IN RECORD, PROCESSING AND EVALUATION OF
GENOMIC SIGNALS

D 2010

BOX COUNTING METHOD IN RECORD, PROCESSING AND EVALUATION OF GENOMIC SIGNALS

VALLA, Martin, Jiří NEDVĚD, Dušan PAVLÍK, Vojtěch ADAM, Jaromír HUBÁLEK et. al.

Basic information

Original name

BOX COUNTING METHOD IN RECORD, PROCESSING AND EVALUATION OF GENOMIC SIGNALS

Authors

VALLA, Martin (203 Czech Republic), Jiří NEDVĚD (203 Czech Republic), Dušan PAVLÍK (203 Czech Republic), Vojtěch ADAM (203 Czech Republic), Jaromír HUBÁLEK (203 Czech Republic), Libuše TRNKOVÁ (203 Czech Republic, belonging to the institution), René KIZEK (203 Czech Republic, guarantor) and Ivo PROVAZNÍK (203 Czech Republic)

Edition

Brno, X. pracovní setkání fyzikálních chemiků a elektrochemiků - sborník příspěvků, p. 243-249, 7 pp. 2010

Publisher

Mendelova univerzita v Brně

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10406 Analytical chemistry

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

RIV identification code

RIV/00216224:14310/10:00040547

Organization unit

Faculty of Science

ISBN

978-80-7375-396-2

UT WoS

000400414900077

Keywords in English

Fractals; dimension; Citrobacter youngae; Homo sapiens

Abstract

V originále

Fractals are geometrical shapes with noninteger dimension and invariation against change of scale factor. For each geometrical shape, one parameter, dimension, can be calculated. For calculation, Box Counting Method (BCM) was chosen. Determination of dimension on one level of resolution is not sufficient, it is necessary to subsequently process it and determine multifractal coefficient. Aim of interest consists in image analysis obtained from linear sequence of DNA code. For analysis itself, sequences of Homo sapiens Atlase and Citrobacter youngae were chosen. Results of calculation are fractal coefficients derived from dimensions of generated structures. This result enables to introduce criterion for sequences determination. Graphical outputs may be also represented as multidimensional alternative transformation of linearly recorded genomic signal. Algorithms are developed in environment of matrix laboratory MATLAB. Origin of data is in public database EMBL (ESI) and GenBank (NCBI).

Links

LC06035, research and development project

Name: Centrum biofyzikální chemie, bioelektrochemie a bioanalýzy. Nové nástroje pro genomiku, proteomiku a biomedicínu.

Investor: Ministry of Education, Youth and Sports of the CR, Centre of Biophysical Chemistry, Bioelectrochemistry and Bioanalysis. New Tools for Genomics, Proteomics and Biomedicine

Citovat

VALLA, Martin, Jiří NEDVĚD, Dušan PAVLÍK, Vojtěch ADAM, Jaromír HUBÁLEK, Libuše TRNKOVÁ, René KIZEK and Ivo PROVAZNÍK. BOX COUNTING METHOD IN RECORD, PROCESSING AND EVALUATION OF GENOMIC SIGNALS. In X. pracovní setkání fyzikálních chemiků a elektrochemiků - sborník příspěvků. Brno: Mendelova univerzita v Brně, 2010, p. 243-249. ISBN 978-80-7375-396-2.

@inproceedings{889991,
   author = {Valla, Martin and Nedvěd, Jiří and Pavlík, Dušan and Adam, Vojtěch and Hubálek, Jaromír and Trnková, Libuše and Kizek, René and Provazník, Ivo},
   address = {Brno},
   booktitle = {X. pracovní setkání fyzikálních chemiků a elektrochemiků - sborník příspěvků},
   keywords = {Fractals; dimension; Citrobacter youngae; Homo sapiens},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Brno},
   isbn = {978-80-7375-396-2},
   pages = {243-249},
   publisher = {Mendelova univerzita v Brně},
   title = {BOX COUNTING METHOD IN RECORD, PROCESSING AND EVALUATION OF GENOMIC SIGNALS},
   year = {2010}
}

TY  - JOUR
ID  - 889991
AU  - Valla, Martin - Nedvěd, Jiří - Pavlík, Dušan - Adam, Vojtěch - Hubálek, Jaromír - Trnková, Libuše - Kizek, René - Provazník, Ivo
PY  - 2010
TI  - BOX COUNTING METHOD IN RECORD, PROCESSING AND EVALUATION OF GENOMIC SIGNALS
PB  - Mendelova univerzita v Brně
CY  - Brno
SN  - 9788073753962
KW  - Fractals
KW  - dimension
KW  - Citrobacter youngae
KW  - Homo sapiens
N2  - Fractals are geometrical shapes with noninteger dimension and invariation against change of scale factor. For each geometrical shape, one parameter, dimension, can be calculated. For calculation, Box Counting Method (BCM) was chosen. Determination of dimension on one level of resolution is not sufficient, it is necessary to subsequently process it and determine multifractal coefficient. Aim of interest consists in image analysis obtained from linear sequence of DNA code. For analysis itself, sequences of Homo sapiens Atlase and Citrobacter youngae were chosen. Results of calculation are fractal coefficients derived from dimensions of generated structures. This result enables to introduce criterion for sequences determination. Graphical outputs may be also represented as multidimensional alternative transformation of linearly recorded genomic signal. Algorithms are developed in environment of matrix laboratory MATLAB. Origin of data is in public database EMBL (ESI) and GenBank (NCBI).
ER  -

VALLA, Martin, Jiří NEDVĚD, Dušan PAVLÍK, Vojtěch ADAM, Jaromír HUBÁLEK, Libuše TRNKOVÁ, René KIZEK and Ivo PROVAZNÍK. BOX COUNTING METHOD IN RECORD, PROCESSING AND EVALUATION OF GENOMIC SIGNALS. In \textit{X. pracovní setkání fyzikálních chemiků a elektrochemiků - sborník příspěvků}. Brno: Mendelova univerzita v Brně, 2010, p.~243-249. ISBN~978-80-7375-396-2.

Detailed Information on Publication Record