Geodesic
Recognition of Latent Periodicity in DNA Sequences
Matematičeskaâ biologiâ i bioinformatika, Tome 8 (2013) no. 2, pp. 502-512.

Voir la notice de l'article provenant de la source Math-Net.Ru

Based on spectral-statistical approach elaborated earlier, the direct methods for recognizing a new type of periodicity in DNA sequences — latent profile periodicity which expands on the notion of approximate tandem repeat — are proposed. Comparison of the proposed methods with the other approaches, taking into account only the indirect indicators of the latent periodicity existence in DNA sequence, was done. 
@article{MBB_2013_8_2_a6,
     author = {M. B. Chaley and V. A. Kutyrkin},
     title = {Recognition of {Latent} {Periodicity} in {DNA} {Sequences}},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {502--512},
     publisher = {mathdoc},
     volume = {8},
     number = {2},
     year = {2013},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/MBB_2013_8_2_a6/}
}
TY  - JOUR
AU  - M. B. Chaley
AU  - V. A. Kutyrkin
TI  - Recognition of Latent Periodicity in DNA Sequences
JO  - Matematičeskaâ biologiâ i bioinformatika
PY  - 2013
SP  - 502
EP  - 512
VL  - 8
IS  - 2
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/item/MBB_2013_8_2_a6/
LA  - ru
ID  - MBB_2013_8_2_a6
ER  - 
%0 Journal Article
%A M. B. Chaley
%A V. A. Kutyrkin
%T Recognition of Latent Periodicity in DNA Sequences
%J Matematičeskaâ biologiâ i bioinformatika
%D 2013
%P 502-512
%V 8
%N 2
%I mathdoc
%U http://geodesic.mathdoc.fr/item/MBB_2013_8_2_a6/
%G ru
%F MBB_2013_8_2_a6
M. B. Chaley; V. A. Kutyrkin. Recognition of Latent Periodicity in DNA Sequences. Matematičeskaâ biologiâ i bioinformatika, Tome 8 (2013) no. 2, pp. 502-512. http://geodesic.mathdoc.fr/item/MBB_2013_8_2_a6/

[1] Korotkov E. V., Korotkova M. A., Tulko J. S., “Latent sequence periodicity of some oncogenes and DNA-binding protein genes”, CABIOS, 13 (1997), 37–44

[2] Korotkov E. V., Korotkova M. A., Kudryashov N. A., “Information decomposition method for analysis of symbolical sequences”, Physical Letters A, 312 (2003), 198–210 | DOI | MR | Zbl

[3] Shelenkov A., Korotkov A., Korotkov E., “MMsat-a database of potential micro-and minisatellites”, Gene, 409 (2008), 53–60 | DOI

[4] Shelenkov A., Skryabin K., Korotkov E., “Search and classification of potential minisatellite sequences from bacterial genomes”, DNA Res., 13 (2006), 89–102 | DOI

[5] Tiwari S., Ramachandran S., Bhattacharya A., Bhattacharya S., Ramaswamy R., “Prediction of probable genes by Fourier analysis of genomic sequences”, Comput. Appl. Biosci., 13 (1997), 263–270

[6] Issac B., Singh H., Kaur H., Raghava G. P. S., “Locating probable genes using Fourier transform approach”, Bioinformatics, 18 (2002), 196–197 | DOI

[7] Sharma D., Issac B., Raghava G. P. S., Ramaswamy R., “Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation”, Bioinformatics, 20 (2004), 1404–1412

[8] Lobzin V. V., Chechetkin V. R., “Poryadok i korrelyatsii v genomnykh posledovatelnostyakh DNK. Spektralnyi podkhod”, UFN, 170 (2000), 57–81 | DOI

[9] Chalei M. B., Nazipova N. N., Kutyrkin V. A., “Sovmestnoe ispolzovanie razlichnykh kriteriev proverki odnorodnosti dlya vyyavleniya skrytoi periodichnosti v biologicheskikh posledovatelnostyakh”, Mat. biologiya i bioinformatika, 2:1 (2007), 20–35 (data obrascheniya: 03.09.2013) http://www.matbio.org/downloads/Chaley2007(2_20).pdf

[10] Chaley M. B., Nazipova N. N., Kutyrkin V. A., “Statistical methods for detecting latent periodicity patterns in biological sequences: the case of small-size samples”, Pattern Recogn. Image Anal., 19 (2009), 358–367 | DOI

[11] Chaley M., Kutyrkin V., “Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences”, Math. Biosci., 211 (2008), 186–204 | DOI | MR | Zbl

[12] Gelfand Y., Rodriguez A., Benson G., “TRDB — the Tandem Repeats Database”, Nucleic Acids Res., 35 (2007), 80–87 (data obrascheniya: 31.07.2013) http://tandem.bu.edu/cgi-bin/trdb/trdb.exe | DOI

[13] Benson G., “Tandem repeats finder: a program to analyze DNA sequences”, Nucl. Acids Res., 27 (1999), 573–580 | DOI

[14] Chalei M. B., Kutyrkin V. A., Tyulbasheva G. E., Teplukhina E. I., Nazipova N. N., “Issledovanie fenomena skrytoi periodichnosti v genomakh eukarioticheskikh organizmov”, Matematicheskaya biologiya i bioinformatika, 8:2 (2013), 480–501 (data obrascheniya: 03.09.2013) http://www.matbio.org/2013/Chaley_8_480.pdf

[15] Kramer G., Matematicheskie metody statistiki, Perevod s angl. pod red. Kolmogorova A. N., Mir, M., 1975, 648 pp. ; Cramer H., Mathematical methods of statistics, Stockholm, 1946 | MR | MR

[16] Chaley M. B., Kutyrkin V. A., “Structure of proteins and latent periodicity in their genes”, Moscow Univ. Biol. Sci. Bull., 65 (2010), 133–135 | DOI

[17] Chaley M., Kutyrkin V., “Profile-Statistical Periodicity of DNA Coding Regions”, DNA Res., 18 (2011), 353–362 | DOI

[18] Kutyrkin V. A., Chalei M. B., “Raspoznavanie razlichnykh urovnei v organizatsii kodirovaniya geneticheskoi informatsii”, Vestnik MGTU im. N. E. Baumana. Seriya Estestvennye nauki, 2011, Spets. vypusk No 2 «Matematicheskoe modelirovanie», 200–215

[19] Kutyrkin V. A., Chalei M. B., “Strukturnye razlichiya kodiruyuschikh i nekodiruyuschikh raionov posledovatelnostei DNK genoma cheloveka”, Vestnik MGTU im. N. E. Baumana. Ser. Estestvennye nauki, 2012, Spets. vypusk No 3 «Matematicheskoe modelirovanie», 146–157

[20] FTG: Fast Fourier Transform based GENE Prediction Server (data obrascheniya: 31.07.2013) http://www.imtech.res.in/raghava/ftg/