Genome sizes and the benford distribution

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Friar, James L ^a   Goldman, Terrance ^a   Pérez Mercader, Juan ^b,c  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; BENFORD DISTRIBUTION; DATA PROCESSING; EUKARYOTE; GENETIC CODE; GENOME SIZE; INFORMATION PROCESSING; MATHEMATICAL PARAMETERS; MOLECULAR DYNAMICS; OPEN READING FRAME; PREDICTION; PROBABILITY; PROKARYOTE;

ANIMALS; ARCHAEA; BACTERIA; EUKARYOTA; EVOLUTION, MOLECULAR; GENOME; GENOME SIZE; OPEN READING FRAMES;

EUKARYOTA; PROKARYOTA;

EID: 84862105854     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036624     Document Type: Article

References (36)

1. Lynch M, (2007) The Origins of Genome Architecture. Sunderland, MA Sinauer.
2. Ahnert SE, Fink TMA, Zinovyev A, (2008) How much non-coding DNA do eukaryotes require? J Theor Biol 252: 587-592.
3. The Genomes Online Database (GOLD) is located at [http://genomesonline.org]. We used the list of complete, published genome projects available in January 2010 as an Excel spreadsheet.
4. Benford F, (1938) The law of anomalous numbers. Proc Amer Phil Soc 78: 551-572.
5. Hamming RW, (1973) Numerical Methods for Scientists and Engineers. New York Dover.
6. Hamming RW, (1970) On the Distribution of Numbers. Bell System Technical Journal 49: 1609-1625.
7. Hill TP, (1995) Base-invariance implies Benford's law. Proc Am Math Soc 123: 887-895.
8. Hill TP, (1995) A statistical derivation of the significant-digit law. Stat Sci 10: 354-363.
9. Berger A, Hill TP, (2011) Benford's law strikes back: no simple explanation in sight for mathematical gem. The Mathematical Intelligencer 33: 85-91.
10. An interesting presentation of many features of Benford's law is given by Ciofalo M, Entropy, Benford's first digit law, and the distribution of everything. See:http://www.din.unipa.it/Struttura/Personale/Profili/Ciofalo.html.
11. Pinkham R, (1961) On the distribution of the first significant digits. Ann Math Statistics 32: 1223-1230.
12. Mattick JS, (2004) RNA regulation: a new genetics? Nat Rev Genetics 5: 316-323.
13. Taft RJ, Pheasant M, Mattick JS, (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29: 288-299.
14. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, et al. (2008) Molecular Biology of the Cell, 5th ed. New York Garland Science, Ch.
15. Beard DA, Qian H, (2008) Chemical Biophysics: Quantitative Analysis of Cellular Systems. Cambridge Cambridge University Press.
16. Phillips R, Kondev J, Theriot J, (2008) Physical Biology of the Cell, 1st ed. New York Garland Science.
17. Goldenfeld N, Woese C, (2011) Life is physics: evolution as a collective phenomenon far from equilibrium. Ann Rev Condens Matter Phys 2: 375-399.
18. Watson JD, Baker TA, Baker SP, Gann A, Levine M, et al. (2008) Molecular Biology of the Gene, 6th ed. San Francisco Pearson/Benjamin Cummings and Cold Spring Harbor Laboratory Press.
19. Brown TA, (2007) Genomes 3. New York Garland Science.
20. McCoy MW, Allen AP, Gillooly JF, (2009) The random nature of genome architecture: predicting open reading frame distributions. PLoS ONE 4: e6456.
21. Hartl D, Ruvolo M, (2012) Genetics: Analysis of Genes and Genomes. Burlington, MA Jones and Bartlett Learning.
22. Davidson EH, (2006) The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. San Diego Academic Press.
23. Fernández A, Lynch M, (2011) Non-adaptive origins of interactome complexity. Nature 474: 502-505.
24. Wang M, Kurland CG, Caetano-Anollés G, (2011) Reductive evolution of proteomes and protein structures. Proc Natl Acad Sci U S A 108: 11954-11958.
25. Wang M, Caetano-Anollés G, (2009) The evolutionary mechanics of domain organization in proteomes and the rise of modularity in the protein world. Structure 17: 66-78.
26. Peterson SN, Hu PC, Bott KF, Hutchison CA III, (1993) A survey of the Mycoplasma genitalium genome by using random sequencing. J Bacteriol 175: 7918-7930.
27. Mushegian AR, Koonin EV, (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93: 10268-10273.
28. Peterson SN, Fraser CM, (2001) The complexity of simplicity. Genome Biol 2: comment 2002.1.
29. Gil R, Silva FJ, Peretó J, Moya A, (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68: 518-537.
30. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, et al. (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103: 425-30.
31. Shannon CE, Weaver W, (1949) The Mathematical Theory of Communication. Urbana, IL University of Illinois Press.
32. Shannon CE, (1948) A Mathematical Theory of Communication. Bell System Technical Journal 27: 379-234.
33. Cover TM, Thomas JA, (1991) Elements of Information Theory. New York Wiley.
34. Rényi A, (1991) Foundations of Probability. New York Dover.
35. Yockey HP, (2005) Information Theory, Evolution, and the Origin of Life. Cambridge Cambridge University Press.
36. Lynch M, Conery JS, (2003) The origins of genome complexity. Science 302: 1401-1404.