Панкратов А.Н., Пятков М.И., Тетуев Р.К., Назипова Н.Н., Дедус Ф.Ф.
Поиск протяженных повторов в геномах на основе спектрально-аналитического метода
Математическая биология и биоинформатика. 2012;7(2):476-492.
doi: 10.17537/2012.7.476.
Список литературы
- Collins FS, Morgan M, Patrinos A. The Human Genome Project: lessons from large-scale biology. Science. 2003;300:286-290. doi: 10.1126/science.1084564
- Podgornaya OI, Ostromishensky DI, Kuznetsova IS, Matveev IV, Komissarov AS. Heterochromatin and centromere structure paradox. Tsitologiya. 2009;51(3):204-211 (in Russ.).
- Fondon JW III, Garner HR. Molecular origins of rapid and continuous morphological evolution. Proc. Nat. Acad. Sci. 2004;101(52):18058-18062.
- Lakich D, Kazazian HH Jr, Antonarakis SE, Gitschier J. Inversions disrupting the factor VIII gene are a common cause of severe haemophilia A. Nat. Genet. 1993;5:236-241.
- Emery AEH. Emery-Dreifuss syndrome. J. Med. Genet. 1989;26:637-641.
- Small K, Iber J, Warren ST. Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Nat. Genet. 1997;16:96-99.
- Richards RI, Holman K, Yu S. and Sutherland GR. Fragile X syndrome unstable element, P(CCG)N, and other simple tandem repeat sequences are binding-sites for specific nuclear proteins. Hum.Mol. Genet. 1993;2:1429-1435.
- Sutherland GR and Richards IR. Simple tandem DNA repeats and human genetic disease. Proc. Natl. Acad. Sci. USA. 1995;92:3636-3641. doi: 10.1073/pnas.92.9.3636
- MitasM. Trinucleotide repeats associated with human disease. Nucleic Acids Res. 1997;25:2245-2253. doi: 10.1093/nar/25.12.2245
- Toth G, Gaspari Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000;10:967-981. doi: 10.1101/gr.10.7.967
- Graur D, Hide WA, Li WH. Is the guinea-pig a rodent? Nature. 1991;351:649-652. doi: 10.1038/351649a0
- Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-425.
- Gidley JW. The lagomorphs an independent order. Science. 1912;36:285-286. doi: 10.1126/science.36.922.285
- Volkov VV, Leont'ev AIu. Biopolimery i kletka (Biopolymers and Cell). 1990;6(6):68-72 (in Russ.). doi: 10.7124/bc.0002A3
- Benson D. Fourier method for biosequence analysis. Nucl. Acid Res. 1991;18:6305-6310. doi: 10.1093/nar/18.21.6305
- Lobzin VV, Chechetkin VR Order and correlations in genomic DNA sequences. The spectral approach. Phys. Usp. 2000;43:55–78.
- Gibbs AJ, McIntyre GA. The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. Eur. J. Biochem. 1970;16:1-11.
- Dedus FF, Kulikova LI, Makhortykh SA, Nazipova NN, Pankratov AN, Tetuev RK. Analytical recognition methods for repeated structures in genomes Doklady Mathematics. 2006;74(3):926-929. doi: 10.1134/S1064562406060354
- Tetuev RK, Dedus FF, Kulikova LI, Makhortykh SA, Nazipova NN, Pankratov AN. Recognition of the structural-functional organization of genetic sequences. MoscowUniversity Computational Mathematics and Cybernetics. 2007;31(2):49-53. doi: 10.3103/S0278641907020021
- Pankratov AN, Gorchakov MA, Dedus FF, Dolotova NS, Kulikova LI, Makhortykh SA, Nazipova NN, Novikova DA, Olshevets MM, Pyatkov MI, Rudnev VR, Tetuev RK, Filippov VV. Spectral Analysis for Identification and Visualization of Repeats in Genetic Sequences. Pattern Recognition and Image Analysis. 2009;19(4):687-692. doi: 10.1134/S105466180904018X
- Tetuev RK, Nazipova NN, Pankratov AN, Dedus FF. Search for Megasatellite Tandem Repeats in Eukaryotic Genomes by Estimation of GC-content Curve Oscillations. Mathematical Biology and Bioinformatics. 2010;5(1):30-42 (in Russ.). doi: 10.17537/2010.5.30
- Nikiforov AF, Suslov SK, Uvarov VB. Classical Orthogonal Polynomials of a Discrete Variable (Scientific Computation). Springer-Verlag, 1991. ISBN-10: 0387511237 doi: 10.1007/978-3-642-74748-9
- Nikiforov AF, Skachkov MV. Methods for computing q-polynomials Matematicheskoe modelirovanie. 2001;13(8):85-94 (in Russ.).
- Hamming RW. Numerical methods for scientists and engineers. MC GRAW-HILL BOOK COMPANY; 1962.
- Tetuev RK, Nazipova NN. Consensus of repeated region of mouse chromosome 6 containing 60 tandem copies of a complex pattern. Repbase Reports. 2010;10(5):776.
- Tetuev RK, Nazipova NN, Dedus FF. Consensus of repeated region of rat chromosome 4 similar to mouse chromosome 6 repeated region, enclosed in the intergenic region between genes Hrh1 and Atg7. Repbase Reports. 2010;10(8):1185.
- Pyatkov MI, Filippov VV, Pankratov AN. Consensus of repeated region of rabbit chromosome 17 containing over 15 huge approximate tandemrepeats. Repbase Reports. 2012;12(3).
- Tilford C, Kuroda-Kawaguchi T, Skaletsky H, Rozen S, Brown L, Rosenberg M, McPherson J,Wylie K, Sekhon M, Kucaba A,Waterston R, Page D. A physical map of the human Y chromosome. Nature. 2001;409:943-945. doi: 10.1038/35057170
- Cavaillé J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B, Bachellerie JP, Brosius J, Hüttenhofer A. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. PNAS. 2000;97(26):14311-14316. doi: 10.1073/pnas.250426397
- Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogentic and Genome Research. 2005;110:462-467. doi: 10.1159/000084979
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403-410. doi: 10.1016/S0022-2836(05)80360-2
- Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-578. doi: 10.1093/nar/27.2.573
- Kolpakov R, Bana G, Kucherov G. mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acid Research. 2003;31:3672-3678. doi: 10.1093/nar/gkg617
- Ogurtsov AY, RoytbergMA, Shabalina SA, Kondrashov AS. OWEN: aligning long collinear regions of genomes. Bioinformatics. 2002;18:1703-1704. doi: 10.1093/bioinformatics/18.12.1703
- Landau GM, Schmidt JP and Sokol D. An Algorithm for Approximate Tandem Repeats. Journal of Computational Biology. 2001;8:1-18. doi: 10.1089/106652701300099038
- Levenshtein VI. Binary codes capable of correcting, deletions, insertions and reversals. Soviet Phys. Dokl. 1966;10:707-710.
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. ClustalWand ClustalX version 2.0. Bioinformatics. 2007;23:2947-2948. doi: 10.1093/bioinformatics/btm404
- Loots GG, Ovcharenko I. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes. Bioinformatics. 2007;23:122-124. doi: 10.1093/bioinformatics/btl546
|
|
|