Comparative testing of DNA segmentation algorithms using benchmark simulations

Molecular Biology and Evolution

Volumn 27, Issue 5, 2010, Pages 1015-1024

  Elhaik, Eran ^a   Graur, Dan ^a   Josić, Kreimir ^b  

^a University of Houston   (United States)

^b UNIVERSITY OF HOUSTON   (United States)

Author keywords

Benchmark simulations; Entropy; GC content; Genome composition; Isochores; Jensen Shannon divergence statistic; Segmentation algorithms

Indexed keywords

CYTOSINE; DNA; GUANINE;

ARTICLE; CHROMOSOME MOSAICISM; COMPARATIVE STUDY; DNA DETERMINATION; ENTROPY; GENE SEQUENCE; GENETIC ALGORITHM; ISOCHORE; QUALITY CONTROL; SIMULATION;

ALGORITHMS; BASE COMPOSITION; BASE PAIRING; BASE SEQUENCE; CHROMOSOMES, HUMAN, PAIR 1; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, NUCLEIC ACID; DNA; GENOME, HUMAN; HUMANS; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

EID: 77951536244     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp307     Document Type: Article

References (41)

1. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Met. 57:289-300.
2. Bernaola-Galván P, Ivanov PC, Nunes Amaral LA, Stanley HE. 2001. Scale invariance in the nonstationarity of human heart rate. Phys Rev Lett. 87:168105.
3. Bernaola-Galván P, Román-Roldán R, Oliver JL. 1996. Compositional segmentation and long-range fractal correlations in DNA sequences. Phys Rev E. 53:5181-5189.
4. Bernardi G. 2000. Isochores and the evolutionary genomics of vertebrates. Gene 241:3-17.
5. Bernardi G. 2001. Misunderstandings about isochores. Part 1. Gene 276:3-13.
6. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F. 1985. The mosaic genome of warm-blooded vertebrates. Science 228:953-958.
7. Boys RJ, Henderson DA. 2004. A Bayesian approach to DNA sequence segmentation. Biometrics 60:573-581.
8. Braun JV, Müller HG. 1998. Statistical methods for DNA sequence segmentation. Statist Sci. 13:142-162.
9. Churchill GA. 1989. Stochastic models for heterogeneous DNA sequences. Bull Math Biol. 51:79-94.
10. Churchill GA. 1992. Hidden Markov chains and the analysis of genome structure. Comput Chem. 16:107-115.
11. Clauset A, Shalizi CR, Newman MEJ. 2009. Power-law distributions in empirical data. SIAM Review. 51:661-703.
12. ClayO, Carels N, Douady C, MacayaG, Bernardi G. 2001. Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses. Gene 276:15-24.
13. Cohen N, Dagan T, Stone L, Graur D. 2005. GC composition of the human genome: in search of isochores. Mol Biol Evol. 22:1260-1272.
14. Cormen TH, Leiserson CE, Rivest RL. 1990. Introduction to algorithms. Cambridge (MA): MIT Press.
15. Costantini M, Clay O, Auletta F, Bernardi G. 2006. An isochore map of human chromosomes. Genome Res. 16:536-541.
16. Cuny G, Soriano P, Macaya G, Bernardi G. 1981. The major components of the mouse and human genomes: preparation, basic properties and compositional heterogeneity. Eur J Biochem. 115:227-233.
17. Eyre-Walker A, Hurst LD. 2001. The evolution of isochores. Nat Rev Genet. 2:549-555.
18. Fickett JW, Torney DC, Wolf DR. 1992. Base compositional structure of genomes. Genomics 13:1056-1064.
19. Fukagawa T, Sugaya K, Matsumoto K, Okumura K, Ando A, Inoko H, Ikemura T. 1995. A boundary of long-range G\+ C% mosaic domains in the human MHC locus: pseudoautosomal boundarylike sequence exists near the boundary. Genomics 25:184-191.
20. Guéguen L. 2005. Sarment: python modules for HMM analysis and partitioning of sequences. Bioinformatics 21:3427-3428.
21. Haiminen N, Mannila H. 2007. Discovering isochores by least-squares optimal segmentation. Gene 394:53-60.
22. Haiminen N, Mannila H, Terzi E. 2007. Comparing segmentations by applying randomization techniques. BMC Bioinformatics 8:171.
23. Häring D, Kypr J. 2001. Mosaic structure of the DNA molecules of the human chromosomes 21 and 22. Mol Biol Rep. 28:9-17. (Pubitemid 32996613)
24. Husmeier D, Wright F. 2002. A Bayesian approach to discriminate between alternative DNA sequence segmentations. Bioinfor-matics 18:226-234
25. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
26. Li W. 2001a. Delineating relative homogeneous G\+C domains in DNA sequences. Gene 276:57-72.
27. Li W. 2001b. New stopping criteria for segmenting DNA sequences. Phys Rev Lett. 86:5815-5818.
28. Li W. 2002. Are isochore sequences homogeneous? Gene 300:129-139.
29. Li W, Bernaola-Galván P, Carpena P, Oliver JL. 2003. Isochores merit the prefix 'iso'. Comput Biol Chem. 27:5-10.
30. Li W, Bernaola-Galván P, Haghighi F, Grosse I. 2002. Applications of recursive segmentation to the analysis of DNA sequences. Comput Chem. 26:491-510.
31. Lin J. 1991. Divergence measures based on the Shannon entropy. IEEE Trans Inf Theory. 37:145-151.
32. Macaya G, Thiery JP, Bernardi G. 1976. An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol. 108:237-254.
33. Nekrutenko A, Li WH. 2000. Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 10:1986-1995.
34. Newman MEJ. 2005. Power laws, Pareto distributions and Zipf's law. Contemp Phys. 46:323-351.
35. Oliver JL, Carpena P, Hackenberg M, Bernaola-Galván P. 2004. IsoFinder: computational prediction of isochores in genome sequences. Nucleic Acids Res. 32:W287-W292.
36. Oliver JL, Román-Roldán R, Perez J, Bernaola-Galván P. 1999. SEGMENT: identifying compositional domains in DNA sequences. Bioinformatics 15:974-979.
37. Pavlicek A, Clay O, Jabbari K, Paces J, Bernardi G. 2002. Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17. FEBS Lett. 511:175-177.
38. Schmidt T, Frishman D. 2008. Assignment of isochores for all completely sequenced vertebrate genomes using a consensus. Genome Biol. 9:R104.
39. Sokal RR, Rohlf FJ. 1995. Biometry. 3rd ed. New York: W.H. Freeman and Company.
40. Wen SY, Zhang CT. 2003. Identification of isochore boundaries in the human genome using the technique of wavelet multi-resolution analysis. Biochem Biophys Res Commun. 311:215-222.
41. Zar JH. 1999. Biostatistical analysis. Upper Saddle River (NJ): Prentice-Hall.