Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.
TLDR
DFT provides a robust detection method for higher order periodicity and is robust with respect to monomer insertions and deletions, random sequence insertions etc.Abstract:
Background
Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity detection and a combination of different methods may improve the prediction accuracy. Discrete Fourier transform (DFT) has been extensively used to study primary periodicities in DNA sequences. Here we investigate the application of DFT method to identify and study alphoid higher order repeats.read more
Citations
More filters
Journal ArticleDOI
Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome.
TL;DR: Fourier transforms and their associated power spectra are used for detecting periodicities and protein-coding genes and are generally regarded as a well established technique, but in the case of P. falciparum the frequency aliases are particularly strong and can mask the 1/3 frequency which is used for gene detecting.
Journal ArticleDOI
Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences.
TL;DR: Fourier analysis of genomic sequences provides the additional insight into mechanisms of hierarchical genome packaging and may be used for verification of the concepts of 3-fold or 5-fold intermediates in virion assembly.
Journal ArticleDOI
Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: how to relate microarray expression data with genomic sequences.
TL;DR: F Fourier analysis of promoter sequences for supercoiling-sensitive genes reveals the tendency in selection of sequences with helical periodicities close to 10nt for relaxation-induced genes and to 11nt for Relaxation-repressed genes.
Journal ArticleDOI
Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique.
V.R. Chechetkin,Vasili Lobzin +1 more
TL;DR: An original discrete double Fourier transform (DDFT) serves for the detection of large-scale genome regularities associated with domains/units at the different levels of hierarchical chromosome folding and can be applied to both genomic DNA sequences and corresponding physico-chemical parameters such as base-pairing free energy.
Journal ArticleDOI
Spectral sum rules and search for periodicities in DNA sequences
TL;DR: It is shown that the restrictions imposed on the significance criteria by the rigorous spectral sum rules can be rationally described with De Finetti distribution, which provides the convenient intermediate asymptotic form between Rayleigh distribution and exact combinatoric theory.
References
More filters
Journal ArticleDOI
Advanced Engineering Mathematics. ByErwin Kreyszig. Pp. xx, 899. 68s. (Wiley.)
Journal ArticleDOI
Long-range correlations in nucleotide sequences
Chung-Kang Peng,Sergey V. Buldyrev,Ary L. Goldberger,Shlomo Havlin,Shlomo Havlin,Francesco Sciortino,Michael Simons,Michael Simons,H. E. Stanley +8 more
TL;DR: This work proposes a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which it refers to as a 'DNA walk', and uncovers a remarkably long-range power law correlation.
Journal ArticleDOI
The DNA sequence of human chromosome 22
Ian Dunham,Nobuyoshi Shimizu,Bruce A. Roe,S. Chissoe,Adrienne Hunt,Joanna Collins,Richard Bruskiewich,David Beare,Michele Clamp,Luc J. Smink,R Ainscough,J P Almeida,A K Babbage,C L Bagguley,J Bailey,K F Barlow,K Bates,O. Beasley,Christine P. Bird,S. Blakey,Anne Bridgeman,D. Buck,J. Burgess,J. Burgess,W Burrill,John Burton,C Carder,Nigel P. Carter,Yuan Chen,Graeme T Clark,S. M. Clegg,V. Cobley,Charlotte G. Cole,R. E. Collier,R. Connor,D. Conroy,N Corby,G. J. Coville,Antony V. Cox,J. C. Davis,J. C. Davis,Elisabeth Dawson,Pawandeep Dhami,C. Dockree,S. J. Dodsworth,Richard Durbin,Andrew D. Ellington,Kathryn L. Evans,J. M. Fey,K. Fleming,Lisa French,A. A. Garner,James G. R. Gilbert,Melanie E. Goward,Darren Grafham,Mark Griffiths,C. Hall,C. Hall,Rebekah Hall,G. Hall-Tamlyn,R. W. Heathcott,R. W. Heathcott,Shuk-Mei Ho,S. Holmes,Sarah E. Hunt,Matthew Jones,J K Kershaw,A M Kimberley,A. King,Gavin K. Laird,Cordelia Langford,Margaret A. Leversha,Christine Lloyd,D. M. Lloyd,I. D. Martyn,M Mashreghi-Mohammadi,Lucy Matthews,O. T. McCann,Joseph L. McClay,Stuart McLaren,Amanda McMurray,Sarah Milne,B. J. Mortimore,C. Odell,R. Pavitt,A. V. Pearce,D. Pearson,Benjamin Phillimore,Sam Phillips,Robert W. Plumb,H. Ramsay,Y. Ramsey,Lesley J. Rogers,Mark T. Ross,Carol Scott,Harminder Sehra,C. D. Skuce,S. Smalley,Michelle Smith,Carol Soderlund,L. Spragon,Charles A. Steward,John Sulston,R. M. Swann,M. Vaudin,M. Vaudin,Melanie M. Wall,J. M. Wallis,M. N. Whiteley,M. N. Whiteley,Dave Willey,L. Williams,Scott M. Williams,H. Williamson,H. Williamson,T. E. Wilmer,Laurens G. Wilming,Charmain L. Wright,Tim Hubbard,David R. Bentley,Stephan Beck,Jane Rogers,Shinsei Minoshima,Kazuhiko Kawasaki,Takashi Sasaki,Shuichi Asakawa,Jun Kudoh,Ai Shintani,Kazunori Shibuya,Y. Yoshizaki,Noriaki Aoki,Susumu Mitsuyama,Feng Chen,L. Chu,Judy S. Crabtree,Stéphane Deschamps,A. Do,T. Do,Angela Dorman,F. Fang,Y. Fu,P. Hu,Axin Hua,Steve Kenton,Hongshing Lai,H. I. Lao,Jennifer Lewis,S. Lewis,Shaoping Lin,P. Loh,Eda Malaj,T. Nguyen,Huaqin Pan,S. Phan,S. Qi,Y. Qian,L. Ray,Q. Ren,S. Shaull,D. Sloan,L. Song,Q. Wang,Yuhang Wang,Z. Wang,Jim White,D. Willingham,H. Wu,Ziyun Yao,M. Zhan,Genwei Zhang,Joseph A. Murray,N. Miller,Patrick Minx,Robert S. Fulton,David W. Johnson,G. Bemis,David Bentley,H. Bradshaw,S. Bourne,Matt Cordes,Zijin Du,Lucinda Fulton,D. Goela,Tina Graves,J. Hawkins,K. Hinds,K. Kemp,Phil Latreille,Dan Layman,Philip Ozersky,Tracy Rohlfing,Paul Scheet,C. Walker,A. Wamsley,Patricia Wohldmann,Kymberlie H. Pepin,Joanne O. Nelson,Ian F Korf,Joseph A. Bedell,LaDeana W. Hillier,Elaine R. Mardis,Robert H. Waterston,Richard K. Wilson,Beverly S. Emanuel,Tamim H. Shaikh,Hiroki Kurahashi,Sulagna C. Saitta,M. L. Budarf,Heather E. McDermid,Alexander Johnson,A. C.C. Wong,Bernice E. Morrow,Lisa Edelmann,U. J. Kim,Hiroaki Shizuya,Melvin I. Simon,Jan P. Dumanski,Myriam Peyrard,Darek Kedra,Eyal Seroussi,Ingegerd Fransson,I. Tapia,Carl E.G. Bruder,K. P. O'Brien +223 more
TL;DR: The sequence of the euchromatic part of human chromosome 22 is reported, which consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.
Journal ArticleDOI
Recognition of protein coding regions in DNA sequences
TL;DR: The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time.
Journal ArticleDOI
The mosaic genome of warm-blooded vertebrates.
Giorgio Bernardi,Birgitta Olofsson,Jan Filipski,Marino Zerial,Julio Salinas,Gérard Cuny,Michele Meunier-Rotival,Francis Rodier +7 more
TL;DR: This approach has revealed that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences.