A probabilistic measure for alignment-free sequence comparison

Bioinformatics

Volumn 20, Issue 18, 2004, Pages 3455-3461

  Pham, Tuan D ^a   Zuegg, Johannes ^b  

^a GRIFFITH UNIVERSITY   (Australia)

^b Alchemia Pty Ltd   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

THREONINE;

ALGORITHM; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA SEQUENCE; ESCHERICHIA COLI K 12; NONHUMAN; OPERON; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ALIGNMENT; SHIGELLA FLEXNERI; STATISTICAL MODEL;

ESCHERICHIA COLI; ESCHERICHIA COLI K12; SHIGELLA; SHIGELLA FLEXNERI;

EID: 12344295510     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth426     Document Type: Article

References (20)

1. 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.
2. Blaisdell,B.E. (1986) A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl Acad. Sci. USA 83, 5155-5159.
3. Cover,T.M. and Thomas,J.A. (1991) Elements of Information Theory. John Wiley and Sons, NY.
4. Ewens,W.J. and Grant,G.R. (2001) Statistical Methods in Bioinformatics. Springer, NY.
5. Felsenstein,J. (1993) PHYLIP (Phylogeny Inference Package), version 3.5c. Distributed by the Author, Department of Genetics, University of Washington, Seattle, WA.
6. Juang,B.H. and Rabiner,L.R. (1985). A probabilistic distance measure for Hidden Markov Models, AT&T Technical Journal, 64, 391-408.
7. Jukes,T.H. and Cantor,C.R. (1969) Evolution of protein molecules. In Munro,H.N. (ed.), Mammalian Protein Metabolism. Academic Press, NY, pp. 21-132.
8. Kimura,M. (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
9. Kroupa,J. (200 ) Measure of divergence of possibility measures. In Proceedings of the 6th Workshop on Uncertainty Processing (WUPES'2003), Hejnice, Czech Republic, pp. 173-181.
10. Li,M., Badger,J.H., Chen,X., Kwong,S., Kearney,P. and Zhang,H. (2001) An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17, 149-154.
11. Li,L., Jin,R., Kok,P.L. and Wan,H. (2004) Pseudo-periodical partitions biological sequences. Bioinformatics, 20, 295-306.
12. Miller,W. (2001) Comparison of genomic DNA sequences: solved and unsolved problems. Bioinformatics, 17, 391-397.
13. Rabiner,L.R. (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 77, 257-286.
14. Rabiner,L. and Juang,B.H. (1993) Fundamentals of Speech Recognition. Prentice Hall, NJ.
15. Stuart,G.W., Moffett,K. and Baker,S. (2002) Integrated gene and species phylogenies from unaligned whole genome protein sequences. Bioinformatics, 18, 100-108.
16. Taha,H.A. (1982) Operations Research: An Introduction. Macmillan, NY.
17. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
18. Vinga,S. and Almeida,J. (2003) Alignment-free sequence comparison - a review. Bioinformatics, 19, 513-523.
19. Wu,T.J., Burke,J.P. and Davison,D.B. (1997) A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. Biometrics, 53, 1431-1439.
20. Wu,T.J., Hsieh,Y.C. and Li,L.A. (2001) Statistical measures of DNA dissimilarity under Markov chain models of base composition. Biometrics, 57, 441-448.