Informational structure of two closely related eukaryotic genomes

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 74, Issue 2, 2006, Pages

  Dehnert, Manuel ^a   Helm, Werner E ^b   Hütt, Marc Thorsten ^a  

^a JACOBS UNIVERSITY BREMEN   (Germany)

^b UNIVERSITY OF APPLIED SCIENCES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CHROMOSOMES; CORRELATION METHODS; DNA SEQUENCES; STATISTICAL METHODS;

EUKARYOTIC GENOMES; GENOME SIGNATURES; RETROTRANSPOSITION; SPECIES SEPARATION;

GENES;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; DNA SEQUENCE; GENETIC CODE; GENETIC VARIABILITY; GENETICS; INFORMATION RETRIEVAL; METHODOLOGY; MOUSE; QUANTITATIVE TRAIT LOCUS; RAT; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

ANIMALS; CHROMOSOME MAPPING; COMPUTER SIMULATION; GENETIC CODE; INFORMATION STORAGE AND RETRIEVAL; MICE; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI; RATS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 33747371129     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.74.021913     Document Type: Article

References (45)

1. J. Jurka, O. Kohany, A. Pavlicek, V. V. Kapitonov, and M. V. Jurka, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0308084100 101, 1268 (2004).
2. S. Yang, A. F. Smit, S. Schwartz, F. Chiaromonte, K. M. Roskin, D. Haussler, W. Miller, and R. C. Hardison, Genome Res. GEREFS 1088-9051 14, 517 (2004).
3. A. L. Price, E. Eskin, and P. A. Pevzner, Genome Res. GEREFS 1088-9051 14, 2245 (2004).
4. J. M. Greally, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 99, 327 (2002).
5. C. Rizzon, G. Marais, M. Gouy, and C. Biemont, Genome Res. GEREFS 1088-9051 12, 400 (2002).
6. C. Chen, A. J. Gentles, J. Jurka, and S. Karlin, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 99, 2930 (2002).
7. I. Ovchinnikov, A. B. Troxel, and G. D. Swergold, Genome Res. GEREFS 1088-9051 11, 2050 (2001).
8. S. Temnykh, G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S. McCouch, Genome Res. GEREFS 1088-9051 11, 1441 (2001).
9. P. W. Messer, P. F. Arndt, and M. Lässig, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.138103 94, 138103 (2005).
10. Y. Zhou and B. Mishra, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 102, 4051 (2005).
11. Y.-H. Chen, S.-L. Nyeo, and C.-Y. Yeh, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.72.011908 72, 011908 (2005).
12. L.-C. Hsieh, L. Luo, F. Ji, and H. C. Lee, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.90.018101 90, 018101 (2003).
13. H.-D. Chen, C.-H. Chang, L.-C. Hsieh, and H.-C. Lee, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.178103 94, 178103 (2005).
14. W. Peng, H. Levine, T. Hwa, and D. A. Kessler, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.69.051911 69, 051911 (2004).
15. S. Nicolay, F. Argoul, M. Touchon, Y. d'Aubenton Carafa, C. Thermes, and A. Arneodo, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.108101 93, 108101 (2004).
16. Y. Xiao, Y. Huang, M. Li, R. Xu, and S. Xiao, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.061913 68, 061913 (2003).
17. I. Grosse, H. Herzel, S. V. Buldyrev, and H. E. Stanley, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.61.5624 61, 5624 (2000).
18. H. Herzel, O. Weiss, and E. N. Trifonov, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/15.3.187 15, 187 (1999).
19. D. Holste, I. Grosse, S. Beirer, P. Schieg, and H. Herzel, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.67.061913 67, 061913 (2003).
20. W. Li and D. Holste, Comput. Biol. Chem. ZZZZZZ 1476-9271 28, 393 (2004).
21. W. Li and D. Holste, Fluct. Noise Lett. ZZZZZZ 0219-4775 4, L453 (2004).
22. S. Karlin and I. Ladunga, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 91, 12832 (1994).
23. S. Karlin and J. Mrázek, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 94, 10227 (1997).
24. A. J. Gentles and S. Karlin, Genome Res. GEREFS 1088-9051 11, 540 (2001).
25. D. T. Pride, R. J. Meinersmann, T. M. Wassenaar, and M. J. Blaser, Genome Res. GEREFS 1088-9051 13, 145 (2003).
26. J. Qi, B. Wang, and B. Hao, J. Mol. Evol. JMEVAU 0022-2844 58, 1 (2004).
27. S. Karlin, A. M. Campbell, and J. Mrázek, Annu. Rev. Genet. ARVGB7 0066-1497 32, 185 (1998).
28. C. Coulondre, J. Miller, P. Farabaugh, and W. Gilbert, Nature (London) NATUAS 0028-0836 274, 775 (1978).
29. A. Razin and A. Riggs, Science SCIEAS 0036-8075 210, 604 (1980).
30. S. Hess, J. Blake, and R. Blake, J. Mol. Biol. JMOBAK 0022-2836 236, 1022 (1994).
31. P. Arndt, C. Burge, and T. Hwa, in Proceedings of the 6th Annual International Conference on Computational Biology (RECOMB 2002) (ACM Press, New York, 2002), pp. 32-38.
32. P. F. Arndt and T. Hwa, Bioinformatics BOINFP 1367-4803 21, 2322 (2005).
33. B. Borstnik and D. Pumpernik, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.71.031913 71, 031913 (2005).
34. B. Borstnik and D. Pumpernik, Europhys. Lett. EULEEJ 0295-5075 10.1209/epl/i2003-10082-6 65, 290 (2004).
35. M. Dehnert, W. E. Helm, and M.-T. Hütt, Physica A PHYADX 0378-4371 327, 535 (2003).
36. M. Dehnert, W. E. Helm, and M.-T. Hütt, Gene GENED6 0378-1119 345, 81 (2005).
37. M. Dehnert, R. Plaumann, W. E. Helm, and M.-T. Hütt, J. Comput. Biol. JCOBEM 1066-5277 10.1089/cmb.2005.12.545 12, 545 (2005).
38. M. I. Jensen-Seaman, T. S. Furey, B. A. Payseur, Y. Lu, K. M. Roskin, C.-F. Chen, M. A. Thomas, D. Haussler, and H. J. Jacob, Genome Res. GEREFS 1088-9051 14, 528 (2004).
39. D. Takai and P. Jones, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.052410099 99, 3740 (2002).
40. A. Smit, R. Hubley, and P. Green, RepeatMasker Open-3.0. at http://www.repeatmasker.org (1996-2004).
41. W. Li and D. Holste, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.71. 041910 71, 041910 (2005).
42. P. Jacobs and P. Lewis, Technical Report NPS55-78-022, Naval Postgraduate School, Monterey, CA, 1978 (unpublished).
43. P. Jacobs and P. Lewis, J. Time Ser. Anal. JTSADL 0143-9782 4, 19 (1983).
44. J. Felsenstein, PHYLIP (Phylogeny Inference Package) version 3.6 (alpha3), distributed by the author. Department of Genome Sciences, University of Washington, Seattle, 2004.
45. R. D. M. Page, CABIOS, Comput. Appl. Biosci. COABER 0266-7061 12, 357 (1996).