Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G + C content

Gene

Volumn 311, Issue 1-2, 2003, Pages 35-42

  Sandberg, Rickard ^a,b   Bränden, Carl Ivar ^a   Ernberg, Ingemar ^a   Cöster, Joakim ^a,b  

^a KAROLINSKA INSTITUTE   (Sweden)

^b Virtual Genetics Laboratory AB   (Sweden)

Author keywords

AU, arbitrary units; C, cytosine; G, guanine; NBC, na ve Bayesian classifier; RSCU, relative synonymous codon usage

Indexed keywords

AMINO ACID; CYSTEINE; GLYCINE;

AMINO ACID ANALYSIS; ARTICLE; CLASSIFICATION; CODON; CORRELATION ANALYSIS; FEASIBILITY STUDY; GENE SEQUENCE; GENETIC CODE; GENOMICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; QUANTITATIVE GENETICS; SEQUENCE ANALYSIS; SPECIES COMPARISON; SPECIES DIFFERENCE; UNINDEXED SEQUENCE;

BACTERIA (MICROORGANISMS); OTHER SEQUENCES; PROKARYOTA;

EID: 0038648028     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(03)00581-X     Document Type: Article

References (22)

1. Almagor H. A Markov analysis of DNA sequences. J. Theor. Biol. 104:1983;633-645.
2. Deschavanne P.J., Giron A., Vilain J., Fagot G., Fertil B. Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol. Biol. Evol. 16:1999;1391-1399.
3. Forsdyke D.R. Different biological species 'broadcast' their DNAs at different (G+C)% 'wavelengths'. J. Theor. Biol. 21:1996;405-417.
4. Forsdyke D.R., Mortimer J.R. Chargaff's legacy. Gene. 261:2000;127-137.
5. Gentles A.S., Karlin S. Genome-Scale Compositional Comparisons in Eukaryotes. Genome Res. 11:2001;540-546.
6. Goldman N. Nucleotide, dinucleotide and trinucleotide frequencies explain patterns observed in chaos game representations of DNA sequences. Nucleic Acids Res. 21:1993;2487-2491.
7. Good I. The Estimation of Probabilities: An Essay on Modern Bayesian Methods. 1965;M.I.T. Press.
8. Grantham R., Gautier C., Gouy M., Mercier R., Pavé A. Nucleic Acids Res. 8:1980;49-62.
9. Karlin S., Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11:1995;283-290.
10. Karlin S., Ladunga I. Comparisons of eukaryotic genomic sequences. Proc. Natl. Acad. Sci. 91:1994;12832-12836.
11. Karlin S., Mrazek J. What drives codon choices in human genes? J. Mol. Biol. 262:1996;459-472.
12. Karlin S., Burge C., Campbell A.M. Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Res. 20:1992;1363-1370.
13. Karlin S., Mrazek J., Campbell A.M. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179:1997;3899-3913.
14. Karlin S., Brocchieri L., Mrazek J., Campbell A.M., Spormann A.M. A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes. Proc. Natl. Acad. Sci. 96:1999;9190-9195.
15. Knight, R.D., Freeland, S.J., Landweber, L.F., 2001. A simple model based on mutation and selection explains trends in codon and amino acid usage and GC composition within and across genomes. Genome Biol. 2, research00100-researc001013.
16. Kraulis, P., 2000. crng1.1: Random-number generators (RNGs) implemented as Python extension types coded in C, http://www.sbc.su.se/∼per/crng/.
17. Lobry J.R. Influence of genomic G+C content on average amino acid composition of proteins from 59 bacterial species. Gene. 205:1997;309-316.
18. Nicolas P., Bize L., Muri F., Hoebeke M., Rodolphe F., Ehrlich S.D., Prum B., Bessières P. Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res. 30:2002;1418-1426.
19. Romero H., Zavala A., Musto H. Codon usage in Chalmydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res. 28:2000;2084-2090.
20. Sandberg R., Winberg G., Bränden C.I., Kaske A., Ernberg I., Cöster J. Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res. 11:2001;1404-1409.
21. Sharp P., Tuohy T., Mosurski K. Nucleic Acids Res. 14:1986;5125-5143.
22. Sueoka N. Correlation between Base Composition of Deoxyribonucleic Acid and Amino Acid Composition of Protein. Proc. Natl. Acad. Sci. 47:1961;1141-1149.