Voir la notice de l'article provenant de la source Math-Net.Ru
@article{MBB_2011_6_2_a2,
author = {V. V. Panyukov and N. N. Nazipova and O. N. Ozoline},
title = {Software {Package} {aSHAPE} as a {Tool} to {Study} the {Spatial} {Conformation} of the {Bacterial} {Genome} {Sites}},
journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
pages = {211--227},
publisher = {mathdoc},
volume = {6},
number = {2},
year = {2011},
language = {ru},
url = {http://geodesic.mathdoc.fr/item/MBB_2011_6_2_a2/}
}
TY - JOUR AU - V. V. Panyukov AU - N. N. Nazipova AU - O. N. Ozoline TI - Software Package aSHAPE as a Tool to Study the Spatial Conformation of the Bacterial Genome Sites JO - Matematičeskaâ biologiâ i bioinformatika PY - 2011 SP - 211 EP - 227 VL - 6 IS - 2 PB - mathdoc UR - http://geodesic.mathdoc.fr/item/MBB_2011_6_2_a2/ LA - ru ID - MBB_2011_6_2_a2 ER -
%0 Journal Article %A V. V. Panyukov %A N. N. Nazipova %A O. N. Ozoline %T Software Package aSHAPE as a Tool to Study the Spatial Conformation of the Bacterial Genome Sites %J Matematičeskaâ biologiâ i bioinformatika %D 2011 %P 211-227 %V 6 %N 2 %I mathdoc %U http://geodesic.mathdoc.fr/item/MBB_2011_6_2_a2/ %G ru %F MBB_2011_6_2_a2
V. V. Panyukov; N. N. Nazipova; O. N. Ozoline. Software Package aSHAPE as a Tool to Study the Spatial Conformation of the Bacterial Genome Sites. Matematičeskaâ biologiâ i bioinformatika, Tome 6 (2011) no. 2, pp. 211-227. http://geodesic.mathdoc.fr/item/MBB_2011_6_2_a2/
[1] Coulombe B. and Zachary F.B., “DNA Bending and Wrapping around RNA Polymerase: a “Revolutionary” Model Describing Transcriptional Mechanisms”, Microbiol. Mol. Biol. Rev., 63 (1999), 457–478
[2] Carmona M., Claverie-Martin F., Magasanik B., “DNA bending and the initiation of transcription at 54-dependent bacterial promoters”, PNAS, 94 (1997), 9568–9572 | DOI
[3] Bolshoy A., Nevo E., “Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters”, Genome Res., 10 (2000), 1185–1193 | DOI
[4] Hirvonen C.A., Ross W., Wozniak C.E., Marasco E., Anthony J.R., Aiyar S.A., Newburn V.H., Richard L., “Gourse Contributions of UP Elements and the Transcription Factor FIS to Expression from the Seven rrn P1 Promoters in Escherichia coli”, J. Bacteriol., 183 (2001), 6305–6314 | DOI
[5] Kozobay-Avraham L., Hosid S., Bolshoy A., “Involvement of DNA curvature in intergenic regions of prokaryotes”, Nucleic Acids Res., 34, 2316–2327 | DOI
[6] Shultzaberger R.K., Chen Z., Lewis K.A., Schneider T.D., “Anatomy of Escherichia coli $\sigma^70$ promoters”, Nucleic Acids Res., 35 (2007), 771–788 | DOI
[7] Pul U., Lux B., Wurm R., Wagner R., “Effect of upstream curvature and transcription factors H-NS and LRP on the efficiency of Escherichia coli rRNA promoters P1 and P2 – a phasing analysis”, Microbiology, 154 (2008), 2546–2558 | DOI
[8] Meysman P., Dang T.H., Laukens K., De Smet R., Wu Y., Marchal K., Engelen K., “Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli”, Nucleic Acids Res., 39 (2011), e6 | DOI
[9] Ozoline O.N., Deev A.A., Trifonov E.N., “DNA bendability – a novel feature in E.coli promoter recognition”, J. Biomol. Struct. Dynamics, 16 (1999), 825–831
[10] Ozoline O.N., Masulis I.S., Buckin V.A., “Deformable elements in promoter DNA as a basis for adaptive conformational transitions”, Biomol. Struct. Dynamics, 18:6 (2001), 1002–1003
[11] Shavkunov K.S., Masulis I.S., Tutukina M.N., Deev A.A., Ozoline O.N., “Gains and unexpected lessons from genome-scale promoter mapping”, Nucleic Acids Res., 37 (2009), 4919–4931 | DOI
[12] Shatzky-Schwartz M., Shakked Z., Luisi B.F., “X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature”, J. Mol. Biol., 267 (1997), 595–623 | DOI
[13] McAteer K., Aceves-Gaona A., Michalczyk R., Buchko G.W., Isern N.G., Silks L.A., Miller J.H., Kennedy M.A., “Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature”, Biopolymers, 75 (2004), 497–511 | DOI
[14] Vlahovicek K., Kajan L., Pongor S., “DNA analysis servers: plot.it, bend.it, model.it and IS”, Nucleic Acids Res., 31:13 (2003), 3686–3687 ; URL: (дата обращения: 01.08.2011) http://hydra.icgeb.trieste.it/dna/index.php | DOI
[15] Faktornyi, diskriminantnyi i klasternyi analiz, ed. I.S. Enyukov, Finansy i statistika, M., 1989
[16] Bolshakov A.A., Karimov R.N., Metody obrabotki mnogomernykh dannykh i vremennykh ryadov, Goryachaya Liniya – Telekom, M., 2007
[17] Fedoseeva V.B., DNK: izgiby dvoinoi spirali: struktura i funktsii URL: (data obrascheniya 01.08.2011) http://medbiol.ru/medbiol/dna_bend/00000a6c.htm#00013419.htm
[18] Zheng G., Xiang-Jun Lu, Wilma K., Olson W.K., “Web 3DNA – a web server for the analysis, reconstruction, and visualization of threedimensional nucleic-acid structures”, Nucleic Acids Research, 37 (2009), W240–W246 | DOI
[19] Strahs D., Schlick T., “Analysis of A-tract bending: Insights into experimental structues by molecular dynamics simulations”, J. Mol. Biol, 301 (2000), 643–663 ; URL: (дата обращения 01.08.2011) http://www.biomath.nyu.edu/index/software/Madbend/index.html | DOI
[20] Xiang-Jun Lu, Shakked Z., Olson W.K., “A-form Conformational Motifs in Ligand-bound DNA Structures”, J. Mol. Biol., 300 (2000), 819–840 | DOI
[21] Dickerson R.E., “DNA bending: the prevalence of kinkiness and the virtues of normality”, Nucleic Acids Res., 26 (1998), 1906–1926 | DOI
[22] Goodsell D.S. and Dickerson R.E., “Bending and curvature calculations in B-DNA”, Nucleic Acids Res., 22:24 (1994), 5497–5503 | DOI
[23] Shpigelman E.S., Trifonov E.N. and Bolshoy A., “CURVATURE: software for the analysis of curved DNA”, Comput. Appl. Biosci., 9 (1993), 435–440
[24] Lavery R., Sklenar H., “The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids”, J. Biomol. Struct. Dyn., 6 (1988), 63–91
[25] Lee S., Park K., Kang C., “Z-curve: a computer program calculating DNA helical axis coordinates for three-dimensional graphic presentation of curvature”, Molecules and Cells, 9:4 (1999), 350–357
[26] Barbic A., Crothers D.M., “Comparison of analyses of DNA curvature”, J. Biomol. Struct. Dyn., 21:1 (2003), 89–97
[27] Herisson J., Payen G., Gherbi R., “A 3D pattern matching algorithm for DNA sequence”, Bioinformatics, 23:6 (2007), 680–686 | DOI
[28] Olson W.K., Bansal M., Burley S.K., Dickerson R.E., Gerstein M., Harvey S.C., Heinemann U., Lu X.-J., Neidle S., Shakked Z., Sklenar H., Suzuki M., Tung C.-S., Westhof E., Wolberger C., Berman H.M., “A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry”, J. Mol. Biol., 313 (2001), 229–237 | DOI
[29] Suzuki M., Amano N., Kakinuma J., Tateno M., “Use of a 3D Structure Data Base for Understanding Sequence-dependent Conformational Aspects of DNA”, J. Mol. Biol., 274 (1997), 421–435 | DOI
[30] Olson W.K., Nucleic acid structural principles URL: (data obrascheniya 01.08.2011) http://128.6.69.24/lnotes/BioPhysChem_week5.pdf
[31] Spravochnik po prikladnoi statistike, v. 2, eds. Aivazyan S.A., Tyurin Yu.N., Finansy i Statistika, M., 1990
[32] Kanhere A., Bansal M., “A novel method for prokaryotic promoter prediction based on DNA stability”, BMC Bioinformatics, 6:1 (2005) | DOI
[33] Wang H., Benham C.J., “Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress”, BMC Bioinformatics, 7:248 (2006)
[34] Sorokin A.A., Osypov A.A., Dzhelyadin T.R., Beskaravainy P.M., Kamzolova S.G., “Electrostatic properties of promoter recognized by E. coli RNA polymerase Esigma70”, J. Bioinform Comput Biol., 4:2 (2006), 455–467 | DOI