DNAskew: Statistical analysis of base compositional asymmetry and prediction of replication boundaries in the genome sequences

Acta Biochimica et Biophysica Sinica

Volumn 36, Issue 1, 2004, Pages 16-20

  Ma, Xiang Ru ^a   Xiao, Shao Bo ^a   Guo, Ai Zhen ^a   Lü, Jian Qiang ^a   Chen, Huan Chun ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Base composition; Bioinformatics; Replication origin; Statistics analysis; Strand asymmetry

Indexed keywords

ARTICLE; BIOINFORMATICS; CODON; COMPUTER PROGRAM; COMPUTER SYSTEM; DNA BASE COMPOSITION; DNA REPLICATION; DNA SEQUENCE; DNA STRAND; GENE FUNCTION; GENOME ANALYSIS; PHYLOGENY; PREDICTION; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; TECHNIQUE;

VERTEBRATA;

EID: 1942439124     PISSN: 05829879     EISSN: None     Source Type: Journal    
DOI: 10.1093/abbs/36.1.16     Document Type: Article

References (23)

1. Chargaff E. Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia, 1950, 6: 201-240
2. Watson JD, Crick FHC. Molecular structure of nucleic acids, a structure for deoxyribose nucleic acid. Nature, 1953, 171: 737-738
3. Lin HJ, Chargaff E. On the denaturation of deoxyribonucleic acid. II. Effects of concentration. Biochim Biophys Acta, 1967, 145: 398-409
4. Sueoka N. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol, 1995, 40: 318-325 (erratum in J Mol Evol, 42: 323)
5. Lobry JR. Properties of a general model of DNA evolution under no-strand-bias conditions. J Mol Evol, 1995, 40: 326-330
6. Liò P. Investigating the relationship between genome structure, composition, and ecology in prokaryotes. Mol Biol Evol, 2002, 19: 789-800
7. Lobry, JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol, 1996, 13: 660-665
8. Mrázek J, Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA, 1998, 95: 3720-3725
9. Bernardi G. Isochores and the evolutionary genomics of vertebrates. Gene, 2000, 241: 3-17
10. Shioiri C, Takahata N. Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry. J Mol Evol, 2001, 53: 364-376
11. Morton BR. Strand asymmetry and codon usage bias in the chloroplast genome of Euglena gracilis. Proc Natl Acad Sci USA, 1999, 96: 5123-5128
12. Rocha EP, Danchin A, Viari A. Universal replication biases in bacteria. Mol Microbiol, 1999, 32: 11-16
13. Rocha EP, Guerdoux-Jamet P, Moszer I, Viari A, Danchin A. Implication of gene distribution in the bacterial chromosome for the bacterial cell factory. J Biotechnol, 2000, 78: 209-219
14. Sueoka N. On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci USA, 1962, 48: 582-592
15. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M et al. The mosaic genome of warm-blooded vertebrates. Science, 1985, 228: 953-958
16. Tisdall J. Beginning Perl for Bioinformatics, California: O'Reilly Publishers, 2001
17. Sharp PM, Li WH. The codon adaptation index - a measure of directional sysonymous codon usage bias, and its potential applications. Nucleic Acids Res, 1987, 15: 1281-1295
18. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-vides J et al. The complete genome sequence of Escherichia coli K-12. Science, 1997, 277: 1453-1474
19. Marsh RC, Worcel A. A DNA fragment containing the origin of replication of the Escherichia coli chromosome. Proc Natl Acad Sci USA, 1977, 74: 2720-2724
20. Prichard MN, Jairath S, Penfold ME, Jeor S, Bohlman MC, Pari GS. Identification of persistent RNA-DNA hybrid structures within the origin of replication of human cytomegalovirus. J Virol, 1998, 72: 6997-7004
21. Vingron M. Bioinformatics needs to adopt statistical thinking. Bioinformatics, 2001, 17: 389-390
22. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res, 1998, 26: 2286-2290
23. Picardeau M, Lobry JR, Hinnebusch BJ. Analyzing DNA strand compositional asymmetry to identify candidate replication origins of borrelia burgdorferi linear and circular plasmids. Genome Res, 2000, 10: 1594-1604