Human-chimpanzee alignment: Ortholog exponentials and paralog power laws

Computational Biology and Chemistry

Volumn 53, Issue PA, 2014, Pages 59-70

  Gao, Kun ^a   Miller, Jonathan ^a  

^a OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

Evolution; Exponential and Power law; Genomic alignment; Length distribution; Orthology and paralogy

Indexed keywords

EVOLUTION; EXPONENTIALS; LENGTH DISTRIBUTIONS; ORTHOLOGS; ORTHOLOGY; PARALOGS; POWER-LAW;

ANIMAL; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETICS; GENOME; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PAN TROGLODYTES; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA;

ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; CONSERVED SEQUENCE; GENOME; HUMANS; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PAN TROGLODYTES; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84908507509     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2014.08.010     Document Type: Article

References (29)

1. A. Albrecht-Buehler Inversions and inverted transpositions as the basis for an almost universal "format" of genome sequences Genomics 90 2007 297 305
2. A.M. Altenhoff, and C. Dessimoz Inferring orthology and paralogy M. Anisimova, Evolutionary Genomics: Statistical and Computational Methods 2012 Springer Science+Business Media (Chapter 9)
3. R. Arratia, and M.S. Waterman Critical phenomena in sequence matching Ann. Probab. 13 4 1985 1236 1249
4. T.A. Brown Molecular phylogenetics Genomes 2nd ed. 2002 Wiley-Liss Oxford (Chapter 16)
5. J.A. Capra, K.S. Pollard, and M. Singh Novel genes exhibit distinct patterns of function acquisition and network integration Genome Biol. 11 R127 2010
6. H.D. Chen, W.L. Fan, S.G. Kong, and H.C. Lee Universal global imprints of genome growth and evolution: equivalent length and cumulative mutation density PLoS ONE 5 4 2010 e9844
7. W. Fitch Distinguishing homologous from analogous proteins Syst. Zool. 19 2 1970 99 113
8. K. Gao, and J. Miller Algebraic distribution of segmental duplication lengths in whole-genome sequence self-alignments PLoS ONE 6 7 2011 e18464
9. A.J. Gibbs, and G.A. McIntyre The diagram, a method for comparing sequences. its use with amino acid and nucleotide sequences Eur. J. Biochem. 16 1970 1 11
10. M.V. Han, J.P. Demuth, C.L. McGrath, C. Casola, and M.W. Hahn Adaptive evolution of young gene duplicates in mammals Genome Res. 19 2009 859 867
11. R.S. Harris Improved pairwise alignment of genomic DNA 2007 The Pennsylvania State University Ph.D. thesis
12. W.J. Kent, R. Baertsch, A. Hinrichs, W. Miller, and D. Haussler Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes Proc. Natl. Acad. Sci. U. S. A. 100 20 2003 11484 11489
13. E.V. Koonin, and Y.I. Wolf The common ancestry of life Biol. Direct 5 64 2010
14. M.V. Koroteev, and J. Miller Scale-free duplication dynamics: a model for ultraduplication Phys. Rev. E 84 061919 2011
15. MV Koroteev, and J Miller Fragmentation dynamics of DNA sequence duplications 2013 arXiv: 1304.1409v3 [math-ph]
16. P.L. Krapivsky, S. Redner, and E. Ben-Naim A Kinetic View of Statistical Physics 2010 Cambridge University Press
17. D.M. Kristensen, Y.I. Wolf, A.R. Mushegian, and E.V. Koonin Computational methods for gene orthology inference Brief. Bioinform. 12 5 2011 379 391
18. W. Kuhn Uber die kinetik des abbaues hochmolekularer ketten Ber. Dtsch. Chem. Ges. 63 1530 1930
19. S. Levy, G. Sutton, P.C. Ng, L. Feuk, and A.L. Halpern The diploid genome sequence of an individual human PLoS Biol. 5 10 2007 e254 10.1371/journal.pbio.0050254
20. M. Lynch The Origins of Genome Architecture 2007 Sinauer
21. F. Massip, and P.F. Arndt Neutral evolution of duplicated DNA: an evolutionary stick-breaking process causes scale-invariant behavior Phys. Rev. Lett. 110 148101 2013
22. E.H. McConkey Orthologous numbering of great ape and human chromosomes is essential for comparative genomics Cytogenet. Genome Res. 105 2004 157 158
23. J. Miller Colossal and super-colossal ultraconservation. IEICE Technical Report Neurocomputing 109 53 2009
24. S. Ohno Evolution by Gene Duplication 1970 Springer-Verlag New York/Heidelberg, Berlin
25. C.P. Ponting, C. Nellaker, and S. Meader Rapid turnover of functional sequence in human and other genomes Annu. Rev. Genom. Human Genet. 12 2011 275 299
26. W. Salerno, P. Havlak, and J. Miller Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments Proc. Natl. Acad. Sci. U. S. A. 103 35 2006 13121 13125
27. E. Taillefer, and J. Miller Exhaustive computation of exact duplications via super and non-nested local maximal repeats J. Bioinform. Comput. Biol. 12 1 2014 1350018
28. R.M. Ziff, and E.D. McGrady The kinetics of cluster fragmentation and depolymerisation J. Phys. A 18 1985 3027
29. E. Zuckerkandl, and L.B. Pauling Molecular Disease, Evolution, and Genic Heterogeneity. Horizons in Biochemistry 1962 Academic Press New York