GENSTYLE: Exploration and analysis of DNA sequences with genomic signature

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Fertil, Bernard ^a   Massin, Matthieu ^a   Lespinats, Sylvain ^a   Devic, Caroline ^a   Dumee, Philippe ^a   Giron, Alain ^a  

^a INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; GENBANK; GENE FREQUENCY; GENE IDENTIFICATION; GENETIC DATABASE; GENOME; GENOMICS; INTERNET; MICROBIAL GROWTH; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES IDENTIFICATION; TAXONOMY; GENE ISOLATION; GENE TRANSFER; MICROORGANISM; CHEMISTRY; CLASSIFICATION; COMPUTER INTERFACE; METHODOLOGY; NUCLEIC ACID DATABASE;

DATABASES, NUCLEIC ACID; GENOMICS; INTERNET; OLIGONUCLEOTIDES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 23144435335     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki489     Document Type: Article

References (34)

1. Karlin,S. and Burge,C. (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet., 11, 283-290.
2. Karlin,S., Campbell,A.M. and Mrazek,J. (1998) Comparative DNA analysis across diverse genomes. Annu. Rev. Genet., 32, 185-225.
3. Deschavanne,P.J., Giron,A., Vilain,J., Fagot,G. and Fertil,B. (1999) Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences. Mol. Biol. Evol., 16, 1391-1399.
4. Sandberg,R., Winberg,G., Branden,C.I., Kaske,A., Ernberg,I. and Coster,J. (2001) Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res., 11, 1404-1409.
5. Almeida,J.S., Carrico,J.A., Maretzek,A., Noble,P.A. and Fletcher,M. (2001) Analysis of genomic sequences by Chaos Game Representation. Bioinformatics, 17, 429-437.
6. Abe,T., Kanaya,S., Kinouchi,M., Ichiba,Y., Kozuki,T. and Ikemura,T. (2002) A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: Self-organizing map of oligonucleotide frequency. Genome Informatics, 13, 12-20.
7. Jernigan,R.W. and Baran,R.H. (2002) Pervasive properties of the genomic signature. BMC Genomics, 3, 23.
8. Wang,Y., Hill,K., Singh,S. and Kari,L. (2005) The spectrum of genomic signatures: From dinucleotides to chaos game representation. Gene, 346, 173-185.
9. Deschavanne,P.J., Giron,A., Vilain,J., Vaury,A. and Fertil,B. (2000) Genomic signature is preserved in short DNA fragments. In Proceedings of the Fourth Annual International Conference on Computational Molecular Biology (RECOMB'00), April 8-11, Tokyo, Japan, pp. 232-233.
10. Chapus,C., Fertil,B., Edwards,S., Giron,A. and Deschavanne,P. (2003) Classification of species based on DNA style. In Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB'03), Berlin, Germany, pp. 147-148.
11. Jeffrey,H.J. (1990) Chaos game representation of gene structure. Nucleic Acids Res., 18, 2163-2170.
12. Jeffrey,H.J. (1992) Chaos game visualization of sequences. Comput. Graph., 16, 25-33.
13. Dutta,C. and Das,J. (1992) Mathematical characterization of Chaos Game Representation. New algorithms for nucleotide sequence analysis. J. Mol. Biol., 228, 715-719.
14. Oliver,J.L., Bernaola-Galvan,P., Guerrero-Garcia,J. and Roman-Roldan,R. (1993) Entropic profiles of DNA sequences through chaos-game-derived images. J. Theor. Biol., 160, 457-470.
15. Edwards,S., Fertil,B., Giron,A. and Deschavanne,P.J. (2002) A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Syst. Biol., 51, 599-613.
16. Yu,Z. and Jiang,P. (2001) Distance, correlation and mutual information among portraits of organisms based on complete genomes. Phys. Lett. A, 286, 34-46.
17. Yap,Y.L., Zhang,X.W. and Danchin,A. (2003) Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling. BMC Bioinformatics, 4, 43.
18. Teeling,H., Meyerdierks,A., Bauer,M., Amann,R. and Glockner,F.O. (2004) Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol., 6, 938-947.
19. Pride,D.T., Meinersmann,R.J., Wassenaar,T.M. and Blaser,M.J. (2003) Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res., 13, 145-158.
20. Dufraigne,C., Fertil,B., Lespinats,S., Giron,A. and Deschavanne,P. (2005) Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res., 33, e6.
21. Tsirigos,A. and Rigoutsos,I. (2005) A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res., 33, 922-933.
22. Hayes,W.S. and Borodovsky,M. (1998) How to interpret an anonymous bacterial genome: Machine learning approach to gene identification. Genome Res., 8, 1154-1171.
23. Nakamura,Y., Itoh,T., Matsuda,H. and Gojobori,T. (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genet., 36, 760-766.
24. Schbath,S., Prum,B. and de Turckheim,E. (1995) Exceptional motifs in different Markov chain models for a statistical analysis of DNA sequences. J. Comput. Biol., 2, 417-437.
25. Phillips,G.J., Arnold,J. and Ivarie,R. (1987) Mono- through hexanucleotide composition of the Escherichia coli genome: A Markov chain analysis. Nucleic Acids Res., 15, 2611-2626.
26. Reinert,G., Schbath,S. and Waterman,M.S. (2000) Probabilistic and statistical properties of words: An overview. J. Comput. Biol., 7, 1-46.
27. Arneodo,A., d'Aubenton-Carafa,Y., Audit,B., Bacry,E., Muzy,J.F. and Thermes,C. (1998) What can we learn with wavelets about DNA sequences? Physica A, 249, 439.
28. Nicolas,P., Bize,L., Muri,F., Hoebeke,M., Rodolphe,F., Ehrlich,S.D., Prum,B. and Bessieres,P. (2002) Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Res., 30, 1418-1426.
29. Campbell,A., Mrazek,J. and Karlin,S. (1999) Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc. Natl Acad. Sci. USA, 96, 9184-9189.
30. Garcia-Vallve,S., Romeu,A. and Palau,J. (2000) Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res., 10, 1719-1725.
31. Ragan,M.A. (2001) On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett., 201, 187-191.
32. Lawrence,J.G. and Ochman,H. (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol., 10, 1-4.
33. Teeling,H., Waldmann,J., Lombardot,T., Bauer,M. and Glockner,F.O. (2004) TETRA: A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics, 5, 163.
34. Flury,B. and Riedwyl,H. (1988) Multivariate Statistics. Chapman and Hall, London.