A rebuttal to the comments on the genome order index and the Z-curve

Biology Direct

Volumn 6, Issue , 2011, Pages

  Zhang, Ren ^a  

^a KEY LABORATORY OF CANCER PREVENTION AND THERAPY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS);

BACTERIAL GENOME; CONFORMATION; GENETICS; NOTE; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; GENOME, BACTERIAL; NUCLEIC ACID CONFORMATION;

EID: 79951555693     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-6-10     Document Type: Note

References (35)

1. Zhang CT, Zhang R. Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucleic Acids Res 1991, 19:6313-6317. 10.1093/nar/19.22.6313, 329145, 1956790.
2. Zhang CT, Zhang R. A nucleotide composition constraint of genome sequences. Comput Biol Chem 2004, 28:149-153. 10.1016/j.compbiolchem.2004.02.002, 15130543.
3. Elhaik E, Graur D, Josic K. 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences. Comput Biol Chem 2008, 32:147. 10.1016/j.compbiolchem.2007.11.003, 18243804.
4. Zhang R. A rebuttal to the comments on the genome order index. Comput Biol Chem 2009, 33:350. 10.1016/j.compbiolchem.2008.11.001, 19097944.
5. Elhaik E, Graur D, Josic K. 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences--a case study of the Z-curve. Biol Direct 2010, 5:10. 10.1186/1745-6150-5-10, 2841071, 20158921.
6. Zhang CT, Gao F, Zhang R. Segmentation algorithm for DNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys 2005, 72:041917. 10.1103/PhysRevE.72.041917, 16383430.
7. Rudner R, Karkas JD, Chargaff E. Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc Natl Acad Sci USA 1968, 60:921-922. 10.1073/pnas.60.3.921, 225140, 4970114.
8. Mitchell D, Bridge R. A test of Chargaff's second rule. Biochem Biophys Res Commun 2006, 340:90-94. 10.1016/j.bbrc.2005.11.160, 16364245.
9. Frank AC, Lobry JR. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 1999, 238:65-77. 10.1016/S0378-1119(99)00297-8, 10570985.
10. Rényi A. On measures of information and entropy. Proc Fourth Berkeley Symp on Math Statist and Prob; Berkeley 1961, 547-561. Univ. of Calif. Press.
11. Zhang Y. Relations between Shannon entropy and genome order index in segmenting DNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys 2009, 79:041918. 10.1103/PhysRevE.79.041918, 19518267.
12. Gao F, Zhang CT. Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics 2008, 9:79. 10.1186/1471-2105-9-79, 2275245, 18237442.
13. Gao F, Zhang CT. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 2007, 23:1866-1867. 10.1093/bioinformatics/btm255, 17496319.
14. Zhang R, Zhang CT. Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea 2005, 1:335-346. 10.1155/2005/509646, 2685548, 15876567.
15. Zhang R, Zhang CT. Multiple replication origins of the archaeon Halobacterium species NRC-1. Biochem Bioph Res Co 2003, 302:728-734.
16. Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R, Bell SD. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 2004, 116:25-38. 10.1016/S0092-8674(03)01034-1, 14718164.
17. Grainge I, Gaudier M, Schuwirth BS, Westcott SL, Sandall J, Atanassova N, Wigley DB. Biochemical analysis of a DNA replication origin in the archaeon Aeropyrum pernix. J Mol Biol 2006, 363:355-369. 10.1016/j.jmb.2006.07.076, 16978641.
18. Zhang CT, Wang J. Recognition of protein coding genes in the yeast genome at better than 95% accuracy based on the Z curve. Nucleic Acids Res 2000, 28:2804-2814. 10.1093/nar/28.14.2804, 102655, 10908339.
19. Yang JY, Zhou Y, Yu ZG, Anh V, Zhou LQ. Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides. BMC Bioinformatics 2008, 9:113. 10.1186/1471-2105-9-113, 2292139, 18294399.
20. Ou HY, Guo FB, Zhang CT. GS-Finder: a program to find bacterial gene start sites with a self-training method. Int J Biochem Cell Biol 2004, 36:535-544. 10.1016/j.biocel.2003.08.013, 14687930.
21. Guo FB, Ou HY, Zhang CT. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res 2003, 31:1780-1789. 10.1093/nar/gkg254, 152858, 12626720.
22. Guo FB, Zhang CT. ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics 2006, 7:9. 10.1186/1471-2105-7-9, 1352377, 16401352.
23. Chen LL, Ou HY, Zhang R, Zhang CT. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes. Biochem Biophys Res Commun 2003, 307:382-388. 10.1016/S0006-291X(03)01192-6, 12859968.
24. Gao F, Zhang CT. Comparison of various algorithms for recognizing short coding sequences of human genes. Bioinformatics 2004, 20:673-681. 10.1093/bioinformatics/btg467, 14764563.
25. Ren SX, Gang F, Jiang XG, Zeng R, Miao YG, Xu H, Zhang YX, Xiong H, Lu G, Lu LF, et al. Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature 2003, 422:888-893. 10.1038/nature01597, 12712204.
26. Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, et al. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 2007, 25:1007-1014. 10.1038/nbt1325, 17704766.
27. He J, Shao XH, Zheng HJ, Li MS, Wang JP, Zhang QY, Li L, Liu ZD, Sun M, Wang SY, Yu ZN. Complete Genome Sequence of Bacillus thuringiensis Mutant Strain BMB171. J Bacteriol 2010, 192:4074-4075. 10.1128/JB.00562-10, 2916366, 20525827.
28. Zhao W, Zhong Y, Yuan H, Wang J, Zheng H, Wang Y, Cen X, Xu F, Bai J, Han X, et al. Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism. Cell Res 2010,
29. Zheng HJ, Lu LD, Wang BF, Pu SY, Zhang XL, Zhu GF, Shi WL, Zhang L, Wang HH, Wang SY, et al. Genetic Basis of Virulence Attenuation Revealed by Comparative Genomic Analysis of Mycobacterium tuberculosis Strain H37Ra versus H37Rv. PLoS One 2008, 3:e2375. 10.1371/journal.pone.0002375, 2440308, 18584054.
30. Lin MF, Deoras AN, Rasmussen MD, Kellis M. Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput Biol 2008, 4:e1000067. 10.1371/journal.pcbi.1000067, 2291194, 18421375.
31. van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W, Berkhout RJM, Wolthers KC, Wertheim-van Dillen PME, Kaandorp J, Spaargaren J, Berkhout B. Identification of a new human coronavirus. Nat Med 2004, 10:368-373. 10.1038/nm1024, 15034574.
32. Pyrc K, Berkhout B, van der Hoek L. The novel human coronaviruses NL63 and HKU1. J Virol 2007, 81:3051-3057. 10.1128/JVI.01466-06, 1866027, 17079323.
33. Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, Li G, Dong BQ, Liu W, Cheung CL, et al. Prevalence and genetic diversity of coronaviruses in bats from China. J Virol 2006, 80:7481-7490. 10.1128/JVI.00697-06, 1563713, 16840328.
34. Wietzorrek A, Schwarz H, Herrmann C, Braun V. The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1. J Bacteriol 2006, 188:1419-1436. 10.1128/JB.188.4.1419-1436.2006, 1367250, 16452425.
35. Lan SF, Huang CH, Chang CH, Liao WC, Lin IH, Jian WN, Wu YG, Chen SY, Wong HC. Characterization of a New Plasmid-Like Prophage in a Pandemic Vibrio parahaemolyticus O3:K6 Strain. Appl Environ Microbiol 2009, 75:2659-2667. 10.1128/AEM.02483-08, 2681713, 19286788.